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+++
title = "Formatting and mounting a volume in Linux"
description = "How to format and mount volume as a hard drive in Linux."
+++
{{% notice info %}}
This guide assumes you associated your SSH Key Pair with the instance
when it was created, and that you are connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
{{% /notice %}}
Once you have [created and attached]({{< relref "creating_and_attaching_a_volume" >}})
your volume, it must be formatted and mounted in your Linux instance to be usable. This
procedure is identical to what would be done when attaching a second
hard drive to a physical machine. In this example, a 10GB volume was
created and attached to the instance. Note that the majority of this
guide is for a newly created volume.
{{% notice note %}}
**If you are attaching an existing volume with data already on it,
skip to [creating a directory and mounting the volume](#mounting-the-volume).**
{{% /notice %}}
#### Formatting the volume
Follow the relevant guide
([Windows]({{< relref "connecting_to_linux_instances_from_windows">}})
| [Mac]({{< relref "connecting_to_linux_instances_from_mac" >}})) for your
operating system to connect to your instance. Formatting and mounting
the volume requires root privileges, so first run the
command `sudo su -` to get a root shell.
{{% panel theme="danger" header="**Running commands as root**" %}}**Extreme care should be taken when running commands as `root.`** It is very easy to permanently delete data or cause irreparable damage to your instance.{{% /panel %}}
{{< figure src="/images/13599376.png" width="700" >}}
Next, you will need to determine what device the volume is presented as
within Linux. Typically this will be `/dev/vdb`, but it is necessary to
verify this to avoid mistakes, especially if you have more than one
volume attached to an instance. The command `fdisk -l` will list the
hard drive devices.
{{< figure src="/images/13599470.png" width="700" >}}
Here there is a completely empty (no partitions) disk device matching
the 10GB size of the volume, so `/dev/vdb` is the correct device.
The `fdisk` utility will first be used to create a single partition.
Run the command `fdisk /dev/vdb` to start the program using the volume
disk device.
{{< figure src="/images/13599477.png" width="700" >}}
Press `n` for new partition and hit enter.
{{< figure src="/images/13599479.png" width="700" >}}
Press `p` for primary partition and hit enter.
{{< figure src="/images/13599482.png" width="700" >}}
Enter `1` for the partition number.
{{< figure src="/images/13599528.png" width="700" >}}
At the next two prompts hit enter to accept the defaults and return to
the main command prompt.
{{< figure src="/images/13599530.png" width="700" >}}
Finally, press `w` followed by return to save the changes and
exit `fdisk`.
{{< figure src="/images/13599533.png" width="700" >}}
Now that a partition has been created, it can be formatted. Here, the
EXT4 filesystem will be used. This is the default filesystem used by
many Linux distributions including CentOS and Ubuntu, and is a good
general choice. An alternate filesystem may be used by running a
different format command. To format the partition using EXT4, run the
command `mkfs.ext4 /dev/vdb1`. You will see a progress message and then
be returned to the shell prompt.
{{< figure src="/images/13599540.png" width="700" >}}
#### Mounting the volume
{{% notice note %}}
If you are attaching a pre-existing volume, start here.
{{% /notice %}}
Finally, the formatted partition must be mounted as a directory to be
used. By convention this is done under `/mnt`, but you may choose to
mount it elsewhere depending on the usage. Here, a directory
called `myvolume` will be created and the volume mounted there. Run the
following commands to make the directory and mount the volume:
{{< highlight bash >}}
mkdir /mnt/myvolume
mnt /dev/vdb1 /mnt/myvolume
{{< /highlight >}}
{{< figure src="/images/13599546.png" width="700" >}}
Running the command `df -h` should then show the new mounted empty
volume.
{{< figure src="/images/13599549.png" width="700" >}}
The volume can now be used.
+++
title = "Handling Data"
description = "How to work with and transfer data to/from HCC resources."
weight = "30"
+++
{{% panel theme="danger" header="**Sensitive and Protected Data**" %}}HCC currently has *no storage* that is suitable for **HIPAA** or other **PID** data sets. Users are not permitted to store such data on HCC machines.{{% /panel %}}
All HCC machines have three separate areas for every user to store data,
each intended for a different purpose. In addition, we have a transfer
service that utilizes [Globus Connect]({{< relref "globus_connect" >}}).
{{< figure src="/images/35325560.png" height="500" class="img-border">}}
---
### Home Directory
{{% notice info %}}
You can access your home directory quickly using the $HOME environmental
variable (i.e. '`cd $HOME'`).
{{% /notice %}}
Your home directory (i.e. `/home/[group]/[username]`) is meant for items
that take up relatively small amounts of space. For example: source
code, program binaries, configuration files, etc. This space is
quota-limited to **20GB per user**. The home directories are backed up
for the purposes of best-effort disaster recovery. This space is not
intended as an area for I/O to active jobs. **/home** is mounted
**read-only** on cluster worker nodes to enforce this policy.
---
### Common Directory
{{% notice info %}}
You can access your common directory quickly using the $COMMON
environmental variable (i.e. '`cd $COMMON`')
{{% /notice %}}
The common directory operates similarly to work and is mounted with
**read and write capability to worker nodes all HCC Clusters**. This
means that any files stored in common can be accessed from Crane and Tusker, making this directory ideal for items that need to be
accessed from multiple clusters such as reference databases and shared
data files.
{{% notice warning %}}
Common is not designed for heavy I/O usage. Please continue to use your
work directory for active job output to ensure the best performance of
your jobs.
{{% /notice %}}
Quotas for common are **30 TB per group**, with larger quotas available
for purchase if needed. However, files stored here will **not be backed
up** and are **not subject to purge** at this time. Please continue to
backup your files to prevent irreparable data loss.
Additional information on using the common directories can be found in
the documentation on [Using the /common File System]({{< relref "using_the_common_file_system" >}})
---
### High Performance Work Directory
{{% notice info %}}
You can access your work directory quickly using the $WORK environmental
variable (i.e. '`cd $WORK'`).
{{% /notice %}}
{{% panel theme="danger" header="**File Loss**" %}}The `/work` directories are **not backed up**. Irreparable data loss is possible with a mis-typed command. See [Preventing File Loss]({{< relref "preventing_file_loss" >}}) for strategies to avoid this.{{% /panel %}}
Every user has a corresponding directory under /work using the same
naming convention as `/home` (i.e. `/work/[group]/[username]`). We
encourage all users to use this space for I/O to running jobs. This
directory can also be used when larger amounts of space are temporarily
needed. There is a **50TB per group quota**; space in /work is shared
among all users. It should be treated as short-term scratch space, and
**is not backed up**. **Please use the `hcc-du` command to check your
own and your group's usage, and back up and clean up your files at
reasonable intervals in $WORK.**
---
### Purge Policy
HCC has a **purge policy on /work** for files that become dormant.
After **6 months of inactivity on a file (26 weeks)**, an automated
purge process will reclaim the used space of these dormant files. HCC
provides the **`hcc-purge`** utility to list both the summary and the
actual file paths of files that have been dormant for **24 weeks**.
This list is periodically generated; the timestamp of the last search
is included in the default summary output when calling `hcc-purge` with
no arguments. No output from `hcc-purge` indicates the last scan did
not find any dormant files. `hcc-purge -l` will use the less pager to
list the matching files for the user. The candidate list can also be
accessed at the following path:` /lustre/purge/current/${USER}.list`.
This list is updated twice a week, on Mondays and Thursdays.
{{% notice warning %}}
`/work` is intended for recent job output and not long term storage. Evidence of circumventing the purge policy by users will result in consequences including account lockout.
{{% /notice %}}
If you have space requirements outside what is currently provided,
please
email <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> and
we will gladly discuss alternatives.
---
### [Attic]({{< relref "using_attic" >}})
Attic is a near line archive available for purchase at HCC. Attic
provides reliable large data storage that is designed to be more
reliable then `/work`, and larger than `/home`. Access to Attic is done
through [Globus Connect]({{< relref "globus_connect" >}}).
More details on Attic can be found on HCC's
<a href="https://hcc.unl.edu/attic" class="external-link">Attic</a>
website.
---
### [Globus Connect]({{< relref "globus_connect" >}})
For moving large amounts of data into or out of HCC resources, users are
highly encouraged to consider using [Globus
Connect]({{< relref "globus_connect" >}}).
---
### Using Box
You can use your [UNL
Box.com]({{< relref "integrating_box_with_hcc" >}}) account to download and
upload files from any of the HCC clusters.
+++
title = "Data for UNMC Users Only"
description= "Data storage options for UNMC users"
weight = 50
+++
{{% panel theme="danger" header="Sensitive and Protected Data" %}} HCC currently has no storage that is suitable for HIPAA or other PID
data sets. Users are not permitted to store such data on HCC machines.
Tusker and Crane have a special directory, only for UNMC users. Please
note that this filesystem is still not suitable for HIPAA or other PID
data sets.
{{% /panel %}}
---
### Transferring files to this machine from UNMC.
You will need to email us
at <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> to
gain access to this machine. Once you do, you can sftp to 10.14.250.1
and upload your files. Note that sftp is your only option. You may use
different sftp utilities depending on your platform you are logging in
from. Email us if you need help with this. Once you are logged in, you
should be at `/volumes/UNMC1ZFS/[group]/[username]`, or
`/home/[group]/[username]`. Both are the same location and you will be
allowed to write files there.
For Windows, learn more about logging in and uploading files
[here](https://hcc-docs.unl.edu/display/HCCDOC/For+Windows+Users).
Using your uploaded files on Tusker or Crane.
---------------------------------------------
Using your
uploaded files is easy. Just go to
`/shared/unmc1/[group]/[username]` and your files will be in the same
place. You may notice that the directory is not available at times. This
is because the unmc1 directory is automounted. This means, if you try to
go to the directory, it will show up. Just "`cd`" to
`/shared/unmc1/[group]/[username]` and all of the files will be
there.
If you have space requirements outside what is currently provided,
please
email <a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a> and
we will gladly discuss alternatives.
+++
title = "Activating HCC Cluster Endpoints"
description = "How to activate HCC endpoints on Globus"
weight = 20
+++
You will not be able to transfer files to or from an HCC endpoint using Globus Connect without first activating the endpoint. Endpoints are available for Tusker (`hcc#tusker`), Crane (`hcc#crane`), and Attic (`hcc#attic`). Follow the instructions below to activate any of these endpoints and begin making transfers.
1. [Sign in](https://www.globus.org/SignIn) to your Globus account using your campus credentials or your Globus ID (if you have one). Then click on 'Endpoints' in the left sidebar.
{{< figure src="/images/Glogin.png" >}}
{{< figure src="/images/endpoints.png" >}}
2. Find the endpoint you want by entering '`hcc#tusker`', '`hcc#crane`', or '`hcc#attic`' in the search box and hit 'enter'. Once you have found and selected the endpoint, click the green 'activate' icon. On the following page, click 'continue'.
{{< figure src="/images/activateEndpoint.png" >}}
{{< figure src="/images/EndpointContinue.png" >}}
3. You will be redirected to the HCC Globus Endpoint Activation page. Enter your *HCC* username and password (the password you usually use to log into the HCC clusters).
{{< figure src="/images/hccEndpoint.png" >}}
4. Next you will be prompted to
provide your *Duo* credentials. If you use the Duo Mobile app on
your smartphone or tablet, select 'Duo Push'. Once you approve the notification that is sent to your phone,
the activation will be complete. If you use a Yubikey for
authentication, select the 'Passcode' option and then press your
Yubikey to complete the activation. Upon successful activation, you
will be redirected to your Globus *Manage Endpoints* page.
{{< figure src="/images/EndpointPush.png" >}}
{{< figure src="/images/endpointComplete.png" >}}
The endpoint should now be ready
and will not have to be activated again for the next 7 days.
To transfer files between any two HCC clusters, you will need to
activate both endpoints individually.
Next, learn how to [make file transfers between HCC endpoints]({{< relref "file_transfers_between_endpoints" >}}) or how to [transfer between HCC endpoints and a personal computer]({{< relref "file_transfers_to_and_from_personal_workstations" >}}).
---
+++
title = "File Sharing"
description = "How to share files using Globus"
weight = 50
+++
If you would like another colleague or researcher to have access to your
data, you may create a shared endpoint on Tusker, Crane, or Attic. You can personally manage access to this endpoint and
give access to anybody with a Globus account (whether or not
they have an HCC account). *Please use this feature responsibly by
sharing only what is necessary and granting access only to trusted
users.*
{{% notice info %}}
Shared endpoints created in your `home` directory on HCC servers (with
the exception of Attic) are *read-only*. You may create readable and
writable shared endpoints in your `work` directory (or `/shared`).
{{% /notice %}}
1. Sign in to your Globus account, click on the 'Endpoints' tab
and search for the endpoint that you will use to host your shared
endpoint. For example, if you would like to share data in your
Tusker `work` directory, search for the `hcc#tusker` endpoint. Once
you have found the endpoint, it will need to be activated if it has
not been already (see [endpoint activation instructions
here]({{< relref "activating_hcc_cluster_endpoints" >}})).
If it is already activated, select the endpoint by clicking on the
name. Then select the 'share' button on the right sidebar.
{{< figure src="/images/sharedEndpoint.png" >}}
{{< figure src="/images/shareButton.png" >}}
2. In the 'Path' box, enter the full path to the directory you
would like to share. Only files under this directory will be shared
to the endpoint users you grant access. Enter a descriptive endpoint
name and provide a
short description of the endpoint if you wish. Finally, click 'Create Share'.
{{< figure src="/images/createShare.png" >}}
3. Type the Globus ID (or group name) of the user (or group) to whom you would like to grant
access to this endpoint. Next enter the *relative path* of the
directory that this user should be able to access. For example, if
the source path of your shared endpoint
is `/work/<groupid>/<userid>/share` but you would like your
colleague to only have access
to `/work/<groupid>/<userid>/share/dataX`, then the 'Path' should be
entered as simply `/dataX`. Finally, click the blue 'Add Permission' button.
You should see the user or group added to the list.
{{< figure src="/images/addPermission.png" >}}
{{< figure src="/images/sharedGroup.png" >}}
---
+++
title = "File Transfers Between Endpoints"
description = "How to transfer files between HCC clusters using Globus"
weight = 30
+++
To transfer files between HCC clusters, you will first need to
[activate]({{< relref "activating_hcc_cluster_endpoints" >}}) the
two endpoints you would like to use (the available endpoints
are: `hcc#tusker,` `hcc#crane, and `hcc#attic)`. Once
that has been completed, follow the steps below to begin transferring
files. (Note: You can also transfer files between an HCC endpoint and
any other Globus endpoint for which you have authorized access. That
may include a [personal
endpoint]({{< relref "file_transfers_to_and_from_personal_workstations" >}}),
a [shared
endpoint]({{< relref "file_sharing" >}}),
or an endpoint on another computing resource or cluster. Once the
endpoints have been activated, the file transfer process is generally
the same regardless of the type of endpoints you use. For demonstration
purposes we use two HCC endpoints.)
1. Once both endpoints for the desired file transfer have been
activated, [sign in](https://www.globus.org/SignIn) to
your Globus account (if you are not already) and select
"Transfer or Sync to.." from the right sidebar. If you have
a small screen, you may have to click the menu icon
first.
{{< figure src="/images/Transfer.png">}}
2. Enter the names of the two endpoints you would like to use, or
select from the drop-down menus (for
example, `hcc#tusker` and `hcc#crane`). Enter the
directory paths for both the source and destination (the 'from' and
'to' paths on the respective endpoints). Press 'Enter' to view files
under these directories. Select the files or directories you would
like to transfer (press *shift* or *control* to make multiple
selections) and click the blue highlighted arrow to start the
transfer.
{{< figure src="/images/startTransfer.png" >}}
3. Globus will display a message when your transfer has completed
(or in the unlikely event that it was unsuccessful), and you will
also receive an email. Select the 'refresh' icon to see your file
in the destination folder.
{{< figure src="/images/transferComplete.png" >}}
---
+++
title = "Integrating Box with HCC"
description = "How to integrate Box with HCC"
weight = 30
+++
UNL has come to an arrangement
with <a href="https://www.box.com/" class="external-link">Box.com</a> to
provide unlimited cloud storage to every student, staff, and faculty
member. This can be useful when used with jobs to automatically upload
results when the job has completed. Combined with
<a href="https://sites.box.com/sync4/" class="external-link">Box Sync</a>,
the uploaded files can be sync'd to your laptop or desktop upon job
completion. The upload and download speed of Box is about 20 to 30 MB/s
in good network traffic conditions. Users can use a tool called lftp to transfer files between HCC clusters and their Box accounts.
---
### Step-by-step guide for Lftp
1. You need to create your UNL [Box.com](https://www.box.com/) account [here](https://box.unl.edu/).
2. Since we are going to be using [webdav](https://en.wikipedia.org/wiki/WebDAV) protocol to access your [Box.com](https://www.box.com/) storage, you need to create an **External Password**. In the [Box.com](https://www.box.com/) interface, you can create it at **[Account Settings](https://unl.app.box.com/settings) > Create External Password.**
{{< figure src="/images/box_create_external_password.png" class="img-border" >}}
3. After logging into the cluster of your choice, load the `lftp` module by entering the command below at the prompt:
{{% panel theme="info" header="Load the lftp module" %}}
{{< highlight bash >}}
module load lftp
{{< /highlight >}}
{{% /panel %}}
4. Connect to Box using your full email as the username and external password you created:
{{% panel theme="info" header="Connect to Box" %}}
{{< highlight bash >}}
lftp -u <username>,<password> ftps://ftp.box.com
{{< /highlight >}}
{{% /panel %}}
5. Test the connection by running the `ls` command. You should see a listing of your Box files. Assuming it works, add a bookmark named "box" to use when connecting later:
{{% panel theme="info" header="Add lftp bookmark" %}}
{{< highlight bash >}}
lftp demo2@unl.edu@ftp.box.com:/> bookmark add box
{{< /highlight >}}
{{% /panel %}}
6. Exit `lftp` by typing `quit`. To reconnect later, use bookmark name:
{{% panel theme="info" header="Connect using bookmark name" %}}
{{< highlight bash >}}
lftp box
{{< /highlight >}}
{{% /panel %}}
7. To upload or download files, use `get` and `put` commands. For example:
{{% panel theme="info" header="Transferring files" %}}
{{< highlight bash >}}
[demo2@login.crane ~]$ lftp box
lftp demo2@unl.edu@ftp.box.com:/> put myfile.txt
lftp demo2@unl.edu@ftp.box.com:/> get my_other_file.txt
{{< /highlight >}}
{{% /panel %}}
8. To download directories, use the `mirror` command. To upload directories, use the `mirror` command with the `-R` option. For example, to download a directory named `my_box-dir` to your current directory:
{{% panel theme="info" header="Download a directory from Box" %}}
{{< highlight bash >}}
[demo2@login.crane ~]$ lftp box
lftp demo2@unl.edu@ftp.box.com:/> mirror my_box_dir
{{< /highlight >}}
{{% /panel %}}
To upload a directory named `my_hcc_dir` to Box, use `mirror` with the `-R` option:
{{% panel theme="info" header="Upload a directory to Box" %}}
{{< highlight bash >}}
[demo2@login.crane ~]$ lftp box
lftp demo2@unl.edu@ftp.box.com:/> mirror -R my_hcc_dir
{{< /highlight >}}
{{% /panel %}}
9. Lftp also supports using scripts to transfer files. This can be used to automatically download or upload files during jobs. For example, create a file called "transfer.sh" with the following lines:
{{% panel theme="info" header="transfer.sh" %}}
{{< highlight bash >}}
open box
get some_input_file.tar.gz
put my_output_file.tar.gz
{{< /highlight >}}
{{% /panel %}}
To run this script, do:
{{% panel theme="info" header="Run transfer.sh" %}}
{{< highlight bash >}}
module load lftp
lftp -f transfer.sh
{{< /highlight >}}
{{% /panel %}}
+++
title = "Jupyter Notebooks on Crane"
description = "How to access and use a Jupyter Notebook"
weight = 20
+++
- [Connecting to Crane] (#connecting-to-crane)
- [Running Code] (#running-code)
- [Opening a Terminal] (#opening-a-terminal)
- [Using Custom Packages] (#using-custom-packages)
## Connecting to Crane
-----------------------
Jupyter defines it's notebooks ("Jupyter Notebooks") as
an open-source web application that allows you to create and share documents that contain live code,
equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation,
statistical modeling, data visualization, machine learning, and much more.
1. To open a Jupyter notebook, [Sign in](https://crane.unl.edu) to crane.unl.edu using your hcc credentials (NOT your
campus credentials).
{{< figure src="/images/jupyterLogin.png" >}}
2. Select your preferred authentication method.
{{< figure src="/images/jupyterPush.png" >}}
3. Choose a job profile. Select "Noteboook via SLURM Job | Small (1 core, 4GB RAM, 8 hours)" for light tasks such as debugging or small-scale testing.
Select the other options based on your computing needs. Note that a SLURM Job will save to your "work" directory.
{{< figure src="/images/jupyterjob.png" >}}
## Running Code
1. Select the "New" dropdown menu and select the file type you want to create.
{{< figure src="/images/jupyterNew.png" >}}
2. A new tab will open, where you can enter your code. Run your code by selecting the "play" icon.
{{< figure src="/images/jupyterCode.png">}}
## Opening a Terminal
1. From your user home page, select "terminal" from the "New" drop-down menu.
{{< figure src="/images/jupyterTerminal.png">}}
2. A terminal opens in a new tab. You can enter [Linux commands] ({{< relref "basic_linux_commands" >}})
at the prompt.
{{< figure src="/images/jupyterTerminal2.png">}}
## Using Custom Packages
Many popular `python` and `R` packages are already installed and available within Jupyter Notebooks.
However, it is possible to install custom packages to be used in notebooks by creating a custom Anaconda
Environment. Detailed information on how to create such an environment can be found at
[Using an Anaconda Environment in a Jupyter Notebook on Crane]({{< relref "using_anaconda_package_manager/#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane" >}}).
---
+++
title = "Running Applications"
description = "How to run various applications on HCC resources."
weight = "20"
+++
{{% children %}}
+++
title = "Allinea Profiling & Debugging Tools"
description = "How to use the Allinea suite of tools for profiling and debugging."
+++
HCC provides both the Allinea Forge suite and Performance Reports to
assist with debugging and profiling C/C++/Fortran code. These tools
support single-threaded, multi-threaded (pthreads/OpenMP), MPI, and CUDA
code. The Allinea Forge suite consists of two programs: DDT for
debugging and MAP for profiling. The Performance Reports software
provides a convenient way to profile HPC applications. It generates an
easy-to-read single-page HTML report.
For information on using each tool, see the following pages.
[Using Allinea Forge via Reverse Connect]({{< relref "using_allinea_forge_via_reverse_connect" >}})
[Allinea Performance Reports]({{< relref "allinea_performance_reports" >}})
+++
title = "Available Software for Crane"
description = "List of available software for crane.unl.edu."
scripts = ["https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/jquery.tablesorter.min.js", "https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/widgets/widget-pager.min.js","https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/widgets/widget-filter.min.js","/js/sort-table.js"]
css = ["http://mottie.github.io/tablesorter/css/theme.default.css","https://mottie.github.io/tablesorter/css/theme.dropbox.css", "https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/css/jquery.tablesorter.pager.min.css","https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/css/filter.formatter.min.css"]
+++
{{% notice tip %}}
HCC provides some software packages via the Singularity container
software. If you do not see a desired package in the module list below,
please check the [Using Singularity]({{< relref "using_singularity" >}})
page for the software list there.
{{% /notice %}}
{{% panel theme="warning" header="Module prerequisites" %}}
If a module lists one or more prerequisites, the prerequisite module(s)
must be loaded before or along with, that module.
For example, the `cdo/2.1` modules requires `compiler/pgi/13.` To load
the cdo module, doing either
`module load compiler/pgi/13`
`module load cdo/2.1`
or
`module load compiler/pgi/13 cdo/2.1` (Note the prerequisite module
**must** be first.)
is acceptable.
{{% /panel %}}
{{% panel theme="info" header="Multiple versions" %}}
Some packages list multiple compilers for prerequisites. This means that
the package has been built with each version of the compilers listed.
{{% /panel %}}
{{% panel theme="warning" header="Custom GPU Anaconda Environment" %}}
If you are using custom GPU Anaconda Environment, the only module you need to load is `anaconda`:
`module load anaconda`
{{% /panel %}}
{{< table url="http://crane-head.unl.edu:8192/lmod/spider/json" >}}
+++
title = "Available Software for Tusker"
description = "List of available software for tusker.unl.edu."
scripts = ["https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/jquery.tablesorter.min.js", "https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/widgets/widget-pager.min.js","https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/js/widgets/widget-filter.min.js","/js/sort-table.js"]
css = ["http://mottie.github.io/tablesorter/css/theme.default.css","https://mottie.github.io/tablesorter/css/theme.dropbox.css", "https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/css/jquery.tablesorter.pager.min.css","https://cdnjs.cloudflare.com/ajax/libs/jquery.tablesorter/2.31.1/css/filter.formatter.min.css"]
+++
{{% notice tip %}}
HCC provides some software packages via the Singularity container
software. If you do not see a desired package in the module list below,
please check the [Using Singularity]({{< relref "using_singularity" >}})
page for the software list there.
{{% /notice %}}
{{% panel theme="warning" header="Module prerequisites" %}}
If a module lists one or more prerequisites, the prerequisite module(s)
must be loaded before or along with, that module.
For example, the `cdo/2.1` modules requires `compiler/pgi/13.` To load
the cdo module, doing either
`module load compiler/pgi/13`
`module load cdo/2.1`
or
`module load compiler/pgi/13 cdo/2.1` (Note the prerequisite module
**must** be first.)
is acceptable.
{{% /panel %}}
{{% panel theme="info" header="Multiple versions" %}}
Some packages list multiple compilers for prerequisites. This means that
the package has been built with each version of the compilers listed.
{{% /panel %}}
{{< table url="http://tusker-head.unl.edu:8192/lmod/spider/json" >}}
+++
title = "Alignment Tools"
description = "How to use various alignment tools on HCC machines"
weight = "52"
+++
{{% children %}}
\ No newline at end of file
+++
title = "BLAST"
description = "How to use BLAST on HCC machines"
weight = "52"
+++
[BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.
The following pages, [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}) and [Running BLAST Alignment]({{<relref "running_blast_alignment" >}}) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
### Useful Information
In order to test the BLAST (blast/2.2) performance on Tusker, we aligned three nucleotide query datasets, `small.fasta`, `medium.fasta` and `large.fasta`, against the non-redundant nucleotide **nt.fasta** database from NCBI. Some statistics about the query datasets and the time and memory resources used for the alignment are shown on the table below:
{{< readfile file="/static/html/blast.html" >}}
1. [HCC-DOCS](index.html)
2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3. [HCC Documentation](HCC-Documentation_332651.html)
4. [Running Applications](Running-Applications_7471153.html)
5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
6. [Biodata Module](Biodata-Module_15171887.html)
<span id="title-text"> HCC-DOCS : Organisms </span>
===================================================
Created by <span class="author"> Adam Caprez</span> on Mar 10, 2016
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Arabidopsis\_thaliana</span>
| Short Name | Source | Build | Type |
|----------------------------------------------|--------|--------|----------------------------|
| ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Main Directory |
| ATH | NCBI | TAIR10 | Main Directory |
| BOWTIE\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ATH | NCBI | TAIR10 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Chromosome Fasta Files |
| CHR\_ATH | NCBI | TAIR10 | Chromosome Fasta Files |
| FAIDX\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Fasta Index .fai File |
| FAIDX\_ATH | NCBI | TAIR10 | Fasta Index .fai File |
| GENOME\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Genome Fasta File |
| GENOME\_ATH | NCBI | TAIR10 | Genome Fasta File |
| PICARD\_ARABIDOPSIS\_THALIANA\_NCBI\_TAIR10 | NCBI | TAIR10 | Picard .dict File |
| PICARD\_ATH | NCBI | TAIR10 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Bacillus\_cereus\_ATCC\_10987</span>
| Short Name | Source | Build | Type |
|------------------------------------------------------------|--------|------------|----------------------------|
| BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Main Directory |
| BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Main Directory |
| BOWTIE\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Chromosome Fasta Files |
| CHR\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Chromosome Fasta Files |
| FAIDX\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Fasta Index .fai File |
| FAIDX\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Fasta Index .fai File |
| GENOME\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Genome Fasta File |
| GENOME\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Genome Fasta File |
| PICARD\_BACILLUS\_CEREUS\_ATCC\_10987 | NCBI | 2004-02-13 | Picard .dict File |
| PICARD\_BACILLUS\_CEREUS\_ATCC\_10987\_NCBI\_2004\_02\_13 | NCBI | 2004-02-13 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Bacillus\_subtilis\_168</span>
| Short Name | Source | Build | Type |
|------------------------------------------------|---------|-------|----------------------------|
| BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Main Directory |
| BOWTIE\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| BSUBT\_168 | Ensembl | EB2 | Main Directory |
| BWA\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BSUBT\_168 | Ensembl | EB2 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Chromosome Fasta Files |
| CHR\_BSUBT\_168 | Ensembl | EB2 | Chromosome Fasta Files |
| FAIDX\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Fasta Index .fai File |
| FAIDX\_BSUBT\_168 | Ensembl | EB2 | Fasta Index .fai File |
| GENOME\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Genome Fasta File |
| GENOME\_BSUBT\_168 | Ensembl | EB2 | Genome Fasta File |
| PICARD\_BACILLUS\_SUBTILIS\_168\_ENSEMBL\_EB2 | Ensembl | EB2 | Picard .dict File |
| PICARD\_BSUBT\_168 | Ensembl | EB2 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Bos\_taurus</span>
| Short Name | Source | Build | Type |
|------------------------------------------|---------|------------|----------------------------|
| BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Main Directory |
| BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Main Directory |
| BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Main Directory |
| BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Main Directory |
| BOWTIE\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_COW | NCBI | UMD\_3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Chromosome Fasta Files |
| CHR\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Chromosome Fasta Files |
| CHR\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Chromosome Fasta Files |
| CHR\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Chromosome Fasta Files |
| CHR\_COW | NCBI | UMD\_3.1 | Chromosome Fasta Files |
| COW | NCBI | UMD\_3.1 | Main Directory |
| FAIDX\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Fasta Index .fai File |
| FAIDX\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Fasta Index .fai File |
| FAIDX\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Fasta Index .fai File |
| FAIDX\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Fasta Index .fai File |
| FAIDX\_COW | NCBI | UMD\_3.1 | Fasta Index .fai File |
| GENOME\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Genome Fasta File |
| GENOME\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Genome Fasta File |
| GENOME\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Genome Fasta File |
| GENOME\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Genome Fasta File |
| GENOME\_COW | NCBI | UMD\_3.1 | Genome Fasta File |
| PICARD\_BOS\_TAURUS\_ENSEMBL\_UMD\_3\_1 | Ensembl | UMD\_3.1 | Picard .dict File |
| PICARD\_BOS\_TAURUS\_ENSEMBL\_UMD3\_1 | Ensembl | UMD3.1 | Picard .dict File |
| PICARD\_BOS\_TAURUS\_NCBI\_UMD\_3\_1 | NCBI | UMD\_3.1 | Picard .dict File |
| PICARD\_BOS\_TAURUS\_NCBI\_UMD\_3\_1\_1 | NCBI | UMD\_3.1.1 | Picard .dict File |
| PICARD\_COW | NCBI | UMD\_3.1 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Caenorhabditis\_elegans</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------|--------|-------|----------------------------|
| BOWTIE\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_CELEGANS | NCBI | WS195 | Bwa\|Bowtie\|Bowtie2 Index |
| CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Main Directory |
| CELEGANS | NCBI | WS195 | Main Directory |
| CHR\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Chromosome Fasta Files |
| CHR\_CELEGANS | NCBI | WS195 | Chromosome Fasta Files |
| FAIDX\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Fasta Index .fai File |
| FAIDX\_CELEGANS | NCBI | WS195 | Fasta Index .fai File |
| GENOME\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Genome Fasta File |
| GENOME\_CELEGANS | NCBI | WS195 | Genome Fasta File |
| PICARD\_CAENORHABDITIS\_ELEGANS\_NCBI\_WS195 | NCBI | WS195 | Picard .dict File |
| PICARD\_CELEGANS | NCBI | WS195 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Canis\_familiaris</span>
| Short Name | Source | Build | Type |
|---------------------------------------------|--------|----------|----------------------------|
| BOWTIE\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_DOG | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
| CHR\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
| CHR\_DOG | NCBI | build3.1 | Chromosome Fasta Files |
| DOG | NCBI | build3.1 | Main Directory |
| FAIDX\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
| FAIDX\_DOG | NCBI | build3.1 | Fasta Index .fai File |
| GENOME\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
| GENOME\_DOG | NCBI | build3.1 | Genome Fasta File |
| PICARD\_CANIS\_FAMILIARIS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
| PICARD\_DOG | NCBI | build3.1 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Danio\_rerio</span>
| Short Name | Source | Build | Type |
|----------------------------------|--------|-------|----------------------------|
| BOWTIE\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_DANIO\_RERIO | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_DANIO\_RERIO | NCBI | Zv9 | Chromosome Fasta Files |
| CHR\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Chromosome Fasta Files |
| DANIO\_RERIO | NCBI | Zv9 | Main Directory |
| DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Main Directory |
| FAIDX\_DANIO\_RERIO | NCBI | Zv9 | Fasta Index .fai File |
| FAIDX\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Fasta Index .fai File |
| GENOME\_DANIO\_RERIO | NCBI | Zv9 | Genome Fasta File |
| GENOME\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Genome Fasta File |
| PICARD\_DANIO\_RERIO | NCBI | Zv9 | Picard .dict File |
| PICARD\_DANIO\_RERIO\_NCBI\_ZV9 | NCBI | Zv9 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Drosophila\_melanogaster</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------------|--------|-----------|----------------------------|
| BOWTIE\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Chromosome Fasta Files |
| CHR\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Chromosome Fasta Files |
| DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Main Directory |
| DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Main Directory |
| FAIDX\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Fasta Index .fai File |
| FAIDX\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Fasta Index .fai File |
| GENOME\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Genome Fasta File |
| GENOME\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Genome Fasta File |
| PICARD\_DROSOPHILA\_MELANOGASTER | NCBI | build5.41 | Picard .dict File |
| PICARD\_DROSOPHILA\_MELANOGASTER\_NCBI\_BUILD5\_41 | NCBI | build5.41 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Enterobacteriophage\_lambda</span>
| Short Name | Source | Build | Type |
|----------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ELAMBDA | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_ELAMBDA | NCBI | 1993-04-28 | Chromosome Fasta Files |
| CHR\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Chromosome Fasta Files |
| ELAMBDA | NCBI | 1993-04-28 | Main Directory |
| ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Main Directory |
| FAIDX\_ELAMBDA | NCBI | 1993-04-28 | Fasta Index .fai File |
| FAIDX\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Fasta Index .fai File |
| GENOME\_ELAMBDA | NCBI | 1993-04-28 | Genome Fasta File |
| GENOME\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Genome Fasta File |
| PICARD\_ELAMBDA | NCBI | 1993-04-28 | Picard .dict File |
| PICARD\_ENTEROBACTERIOPHAGE\_LAMBDA\_NCBI\_1993\_04\_28 | NCBI | 1993-04-28 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Equus\_caballus</span>
| Short Name | Source | Build | Type |
|--------------------------------------------|--------|-----------|----------------------------|
| BOWTIE\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_HORSE | NCBI | EquCab2.0 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Chromosome Fasta Files |
| CHR\_HORSE | NCBI | EquCab2.0 | Chromosome Fasta Files |
| EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Main Directory |
| FAIDX\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Fasta Index .fai File |
| FAIDX\_HORSE | NCBI | EquCab2.0 | Fasta Index .fai File |
| GENOME\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Genome Fasta File |
| GENOME\_HORSE | NCBI | EquCab2.0 | Genome Fasta File |
| HORSE | NCBI | EquCab2.0 | Main Directory |
| PICARD\_EQUUS\_CABALLUS\_NCBI\_EQUCAB2\_0 | NCBI | EquCab2.0 | Picard .dict File |
| PICARD\_HORSE | NCBI | EquCab2.0 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Escherichia\_coli\_K\_12\_DH10B</span>
| Short Name | Source | Build | Type |
|--------------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Chromosome Fasta Files |
| CHR\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Chromosome Fasta Files |
| ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Main Directory |
| ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Main Directory |
| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Fasta Index .fai File |
| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Fasta Index .fai File |
| GENOME\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Genome Fasta File |
| GENOME\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Genome Fasta File |
| PICARD\_ESCHERICHIA\_COLI\_K\_12\_DH10B | NCBI | 2008-03-17 | Picard .dict File |
| PICARD\_ESCHERICHIA\_COLI\_K\_12\_DH10B\_NCBI\_2008\_03\_17 | NCBI | 2008-03-17 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Escherichia\_coli\_K\_12\_MG1655</span>
| Short Name | Source | Build | Type |
|---------------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Chromosome Fasta Files |
| CHR\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Chromosome Fasta Files |
| ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Main Directory |
| ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Main Directory |
| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Fasta Index .fai File |
| FAIDX\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Fasta Index .fai File |
| GENOME\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Genome Fasta File |
| GENOME\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Genome Fasta File |
| PICARD\_ESCHERICHIA\_COLI\_K\_12\_MG1655 | NCBI | 2001-10-15 | Picard .dict File |
| PICARD\_ESCHERICHIA\_COLI\_K\_12\_MG1655\_NCBI\_2001\_10\_15 | NCBI | 2001-10-15 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Gallus\_gallus</span>
| Short Name | Source | Build | Type |
|------------------------------------------|--------|----------|----------------------------|
| BOWTIE\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_GALLUS\_GALLUS | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_GALLUS\_GALLUS | NCBI | build3.1 | Chromosome Fasta Files |
| CHR\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
| FAIDX\_GALLUS\_GALLUS | NCBI | build3.1 | Fasta Index .fai File |
| FAIDX\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
| GALLUS\_GALLUS | NCBI | build3.1 | Main Directory |
| GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
| GENOME\_GALLUS\_GALLUS | NCBI | build3.1 | Genome Fasta File |
| GENOME\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
| PICARD\_GALLUS\_GALLUS | NCBI | build3.1 | Picard .dict File |
| PICARD\_GALLUS\_GALLUS\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Glycine\_max</span>
| Short Name | Source | Build | Type |
|--------------------------------------|---------|-------|----------------------------|
| BOWTIE\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_SOYBEAN | Ensembl | Gm01 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Chromosome Fasta Files |
| CHR\_SOYBEAN | Ensembl | Gm01 | Chromosome Fasta Files |
| FAIDX\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Fasta Index .fai File |
| FAIDX\_SOYBEAN | Ensembl | Gm01 | Fasta Index .fai File |
| GENOME\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Genome Fasta File |
| GENOME\_SOYBEAN | Ensembl | Gm01 | Genome Fasta File |
| GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Main Directory |
| PICARD\_GLYCINE\_MAX\_ENSEMBL\_GM01 | Ensembl | Gm01 | Picard .dict File |
| PICARD\_SOYBEAN | Ensembl | Gm01 | Picard .dict File |
| SOYBEAN | Ensembl | Gm01 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Homo\_sapiens</span>
| Short Name | Source | Build | Type |
|------------------------------------------|--------|-----------|----------------------------|
| BOWTIE\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_HUMAN | NCBI | build37.2 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Chromosome Fasta Files |
| CHR\_HUMAN | NCBI | build37.2 | Chromosome Fasta Files |
| FAIDX\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Fasta Index .fai File |
| FAIDX\_HUMAN | NCBI | build37.2 | Fasta Index .fai File |
| GENOME\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Genome Fasta File |
| GENOME\_HUMAN | NCBI | build37.2 | Genome Fasta File |
| HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Main Directory |
| HUMAN | NCBI | build37.2 | Main Directory |
| PICARD\_HOMO\_SAPIENS\_NCBI\_BUILD37\_2 | NCBI | build37.2 | Picard .dict File |
| PICARD\_HUMAN | NCBI | build37.2 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Macaca\_mulatta</span>
| Short Name | Source | Build | Type |
|--------------------------------------------|---------|---------|----------------------------|
| BOWTIE\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Chromosome Fasta Files |
| CHR\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Chromosome Fasta Files |
| FAIDX\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Fasta Index .fai File |
| FAIDX\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Fasta Index .fai File |
| GENOME\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Genome Fasta File |
| GENOME\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Genome Fasta File |
| MACACA\_MULATTA | Ensembl | Mmul\_1 | Main Directory |
| MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Main Directory |
| PICARD\_MACACA\_MULATTA | Ensembl | Mmul\_1 | Picard .dict File |
| PICARD\_MACACA\_MULATTA\_ENSEMBL\_MMUL\_1 | Ensembl | Mmul\_1 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Mus\_musculus</span>
| Short Name | Source | Build | Type |
|--------------------------------------|--------|--------|----------------------------|
| BOWTIE\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MOUSE | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_MOUSE | NCBI | GRCm38 | Chromosome Fasta Files |
| CHR\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Chromosome Fasta Files |
| FAIDX\_MOUSE | NCBI | GRCm38 | Fasta Index .fai File |
| FAIDX\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Fasta Index .fai File |
| GENOME\_MOUSE | NCBI | GRCm38 | Genome Fasta File |
| GENOME\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Genome Fasta File |
| MOUSE | NCBI | GRCm38 | Main Directory |
| MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Main Directory |
| PICARD\_MOUSE | NCBI | GRCm38 | Picard .dict File |
| PICARD\_MUS\_MUSCULUS\_NCBI\_GRCM38 | NCBI | GRCm38 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Mycobacterium\_tuberculosis\_H37RV</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Chromosome Fasta Files |
| CHR\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Chromosome Fasta Files |
| FAIDX\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Fasta Index .fai File |
| FAIDX\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Fasta Index .fai File |
| GENOME\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Genome Fasta File |
| GENOME\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Genome Fasta File |
| MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Main Directory |
| MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Main Directory |
| PICARD\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV | NCBI | 2001-09-07 | Picard .dict File |
| PICARD\_MYCOBACTERIUM\_TUBERCULOSIS\_H37RV\_NCBI\_2001\_09\_07 | NCBI | 2001-09-07 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Oryza\_sativa\_japonica</span>
| Short Name | Source | Build | Type |
|--------------------------------------------------------|---------|-----------|----------------------------|
| BOWTIE\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_RICE | Ensembl | IRGSP-1.0 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Chromosome Fasta Files |
| CHR\_RICE | Ensembl | IRGSP-1.0 | Chromosome Fasta Files |
| FAIDX\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Fasta Index .fai File |
| FAIDX\_RICE | Ensembl | IRGSP-1.0 | Fasta Index .fai File |
| GENOME\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Genome Fasta File |
| GENOME\_RICE | Ensembl | IRGSP-1.0 | Genome Fasta File |
| ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Main Directory |
| PICARD\_ORYZA\_SATIVA\_JAPONICA\_ENSEMBL\_IRGSP\_1\_0 | Ensembl | IRGSP-1.0 | Picard .dict File |
| PICARD\_RICE | Ensembl | IRGSP-1.0 | Picard .dict File |
| RICE | Ensembl | IRGSP-1.0 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Pan\_troglodytes</span>
| Short Name | Source | Build | Type |
|--------------------------------------------|--------|----------|----------------------------|
| BOWTIE\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PAN\_TROGLODYTES | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_PAN\_TROGLODYTES | NCBI | build3.1 | Chromosome Fasta Files |
| CHR\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
| FAIDX\_PAN\_TROGLODYTES | NCBI | build3.1 | Fasta Index .fai File |
| FAIDX\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
| GENOME\_PAN\_TROGLODYTES | NCBI | build3.1 | Genome Fasta File |
| GENOME\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
| PAN\_TROGLODYTES | NCBI | build3.1 | Main Directory |
| PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
| PICARD\_PAN\_TROGLODYTES | NCBI | build3.1 | Picard .dict File |
| PICARD\_PAN\_TROGLODYTES\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">PhiX</span>
| Short Name | Source | Build | Type |
|------------------------------|----------|-------|----------------------------|
| BOWTIE\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PHIX | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_PHIX | Illumina | RTA | Chromosome Fasta Files |
| CHR\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Chromosome Fasta Files |
| FAIDX\_PHIX | Illumina | RTA | Fasta Index .fai File |
| FAIDX\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Fasta Index .fai File |
| GENOME\_PHIX | Illumina | RTA | Genome Fasta File |
| GENOME\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Genome Fasta File |
| PHIX | Illumina | RTA | Main Directory |
| PHIX\_ILLUMINA\_RTA | Illumina | RTA | Main Directory |
| PICARD\_PHIX | Illumina | RTA | Picard .dict File |
| PICARD\_PHIX\_ILLUMINA\_RTA | Illumina | RTA | Picard .dict File |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Pseudomonas\_aeruginosa\_PAO1</span>
| Short Name | Source | Build | Type |
|------------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Chromosome Fasta Files |
| CHR\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Chromosome Fasta Files |
| FAIDX\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Fasta Index .fai File |
| FAIDX\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Fasta Index .fai File |
| GENOME\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Genome Fasta File |
| GENOME\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Genome Fasta File |
| PICARD\_PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Picard .dict File |
| PICARD\_PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Picard .dict File |
| PSEUDOMONAS\_AERUGINOSA\_PAO1 | NCBI | 2000-09-13 | Main Directory |
| PSEUDOMONAS\_AERUGINOSA\_PAO1\_NCBI\_2000\_09\_13 | NCBI | 2000-09-13 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Rattus\_norvegicus</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------|--------|-----------|----------------------------|
| BOWTIE\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_RAT | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_RAT | NCBI | Rnor\_5.0 | Chromosome Fasta Files |
| CHR\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Chromosome Fasta Files |
| CHR\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Chromosome Fasta Files |
| FAIDX\_RAT | NCBI | Rnor\_5.0 | Fasta Index .fai File |
| FAIDX\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Fasta Index .fai File |
| FAIDX\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Fasta Index .fai File |
| GENOME\_RAT | NCBI | Rnor\_5.0 | Genome Fasta File |
| GENOME\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Genome Fasta File |
| GENOME\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Genome Fasta File |
| PICARD\_RAT | NCBI | Rnor\_5.0 | Picard .dict File |
| PICARD\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Picard .dict File |
| PICARD\_RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Picard .dict File |
| RAT | NCBI | Rnor\_5.0 | Main Directory |
| RATTUS\_NORVEGICUS\_NCBI\_RNOR\_5\_0 | NCBI | Rnor\_5.0 | Main Directory |
| RATTUS\_NORVEGICUS\_NCBI\_RNOR\_6\_0 | NCBI | Rnor\_6.0 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Saccharomyces\_cerevisiae</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------------|--------|----------|----------------------------|
| BOWTIE\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_YEAST | NCBI | build3.1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Chromosome Fasta Files |
| CHR\_YEAST | NCBI | build3.1 | Chromosome Fasta Files |
| FAIDX\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Fasta Index .fai File |
| FAIDX\_YEAST | NCBI | build3.1 | Fasta Index .fai File |
| GENOME\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Genome Fasta File |
| GENOME\_YEAST | NCBI | build3.1 | Genome Fasta File |
| PICARD\_SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Picard .dict File |
| PICARD\_YEAST | NCBI | build3.1 | Picard .dict File |
| SACCHAROMYCES\_CEREVISIAE\_NCBI\_BUILD3\_1 | NCBI | build3.1 | Main Directory |
| YEAST | NCBI | build3.1 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Sorghum\_bicolor</span>
| Short Name | Source | Build | Type |
|------------------------------------------|---------|-------|----------------------------|
| BOWTIE\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_SORGHUM | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_SORGHUM | Ensembl | Sbi1 | Chromosome Fasta Files |
| CHR\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Chromosome Fasta Files |
| FAIDX\_SORGHUM | Ensembl | Sbi1 | Fasta Index .fai File |
| FAIDX\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Fasta Index .fai File |
| GENOME\_SORGHUM | Ensembl | Sbi1 | Genome Fasta File |
| GENOME\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Genome Fasta File |
| PICARD\_SORGHUM | Ensembl | Sbi1 | Picard .dict File |
| PICARD\_SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Picard .dict File |
| SORGHUM | Ensembl | Sbi1 | Main Directory |
| SORGHUM\_BICOLOR\_ENSEMBL\_SBI1 | Ensembl | Sbi1 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Staphylococcus\_aureus\_NCTC\_8325</span>
| Short Name | Source | Build | Type |
|-----------------------------------------------------------------|--------|------------|----------------------------|
| BOWTIE\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Chromosome Fasta Files |
| CHR\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Chromosome Fasta Files |
| FAIDX\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Fasta Index .fai File |
| FAIDX\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Fasta Index .fai File |
| GENOME\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Genome Fasta File |
| GENOME\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Genome Fasta File |
| PICARD\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Picard .dict File |
| PICARD\_STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Picard .dict File |
| STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325 | NCBI | 2006-02-13 | Main Directory |
| STAPHYLOCOCCUS\_AUREUS\_NCTC\_8325\_NCBI\_2006\_02\_13 | NCBI | 2006-02-13 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Sus\_scrofa</span>
| Short Name | Source | Build | Type |
|------------------------------------------|--------|-------------|----------------------------|
| BOWTIE\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_PIG | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_PIG | NCBI | Sscrofa10.2 | Chromosome Fasta Files |
| CHR\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Chromosome Fasta Files |
| FAIDX\_PIG | NCBI | Sscrofa10.2 | Fasta Index .fai File |
| FAIDX\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Fasta Index .fai File |
| GENOME\_PIG | NCBI | Sscrofa10.2 | Genome Fasta File |
| GENOME\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Genome Fasta File |
| PICARD\_PIG | NCBI | Sscrofa10.2 | Picard .dict File |
| PICARD\_SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Picard .dict File |
| PIG | NCBI | Sscrofa10.2 | Main Directory |
| SUS\_SCROFA\_NCBI\_SSCROFA10\_2 | NCBI | Sscrofa10.2 | Main Directory |
<span
class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
class="expand-control-text">Zea\_mays</span>
| Short Name | Source | Build | Type |
|------------------------------------|---------|-------|----------------------------|
| BOWTIE\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| BOWTIE2\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_MAIZE | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| BWA\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Bwa\|Bowtie\|Bowtie2 Index |
| CHR\_MAIZE | Ensembl | AGPv3 | Chromosome Fasta Files |
| CHR\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Chromosome Fasta Files |
| FAIDX\_MAIZE | Ensembl | AGPv3 | Fasta Index .fai File |
| FAIDX\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Fasta Index .fai File |
| GENOME\_MAIZE | Ensembl | AGPv3 | Genome Fasta File |
| GENOME\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Genome Fasta File |
| MAIZE | Ensembl | AGPv3 | Main Directory |
| PICARD\_MAIZE | Ensembl | AGPv3 | Picard .dict File |
| PICARD\_ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Picard .dict File |
| ZEA\_MAYS\_ENSEMBL\_AGPV3 | Ensembl | AGPv3 | Main Directory |
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane.xml](attachments/15171894/15171895.xml)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Arabidopsis\_thaliana.xsl](attachments/15171894/15171896.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Bacillus\_cereus\_ATCC\_10987.xsl](attachments/15171894/15171897.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Bacillus\_subtilis\_168.xsl](attachments/15171894/15171898.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Bos\_taurus.xsl](attachments/15171894/15171899.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Caenorhabditis\_elegans.xsl](attachments/15171894/15171900.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Canis\_familiaris.xsl](attachments/15171894/15171901.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Danio\_rerio.xsl](attachments/15171894/15171902.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Drosophila\_melanogaster.xsl](attachments/15171894/15171903.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Enterobacteriophage\_lambda.xsl](attachments/15171894/15171904.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Equus\_caballus.xsl](attachments/15171894/15171905.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Escherichia\_coli\_K\_12\_DH10B.xsl](attachments/15171894/15171906.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Escherichia\_coli\_K\_12\_MG1655.xsl](attachments/15171894/15171907.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Gallus\_gallus.xsl](attachments/15171894/15171908.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Glycine\_max.xsl](attachments/15171894/15171909.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Homo\_sapiens.xsl](attachments/15171894/15171910.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Macaca\_mulatta.xsl](attachments/15171894/15171911.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Mus\_musculus.xsl](attachments/15171894/15171912.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Mycobacterium\_tuberculosis\_H37RV.xsl](attachments/15171894/15171913.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Oryza\_sativa\_japonica.xsl](attachments/15171894/15171914.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Pan\_troglodytes.xsl](attachments/15171894/15171915.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_PhiX.xsl](attachments/15171894/15171916.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Pseudomonas\_aeruginosa\_PAO1.xsl](attachments/15171894/15171917.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Rattus\_norvegicus.xsl](attachments/15171894/15171918.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Saccharomyces\_cerevisiae.xsl](attachments/15171894/15171919.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Sorghum\_bicolor.xsl](attachments/15171894/15171920.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Staphylococcus\_aureus\_NCTC\_8325.xsl](attachments/15171894/15171921.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Sus\_scrofa.xsl](attachments/15171894/15171922.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane\_Zea\_mays.xsl](attachments/15171894/15171923.xsl)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane.xml](attachments/15171894/35324389.xml) (text/xml)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[biodata\_crane.xml](attachments/15171894/35324388.xml) (text/xml)
+++
title = "Data Manipulation Tools"
description = "How to use data manipulation tools on HCC machines"
weight = "52"
+++
{{% children %}}
\ No newline at end of file
+++
title = "De Novo Assembly Tools"
description = "How to use de novo assembly tools on HCC machines"
weight = "52"
+++
{{% children %}}
+++
title = "Running Trinity in Multiple Steps"
description = "How to run Trinity in multiple steps on HCC resources"
weight = "10"
+++
## Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of RAM
The first step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
{{% panel header="`trinity_step1.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Trinity_Step1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Trinity_Step1.%J.out
#SBATCH --error=Trinity_Step1.%J.err
module load trinity/2.6
Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
{{< /highlight >}}
{{% /panel %}}
The second step of running Trinity is to run Trinity with the option **--no_run_quantifygraph**:
{{% panel header="`trinity_step2.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Trinity_Step2
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Trinity_Step2.%J.out
#SBATCH --error=Trinity_Step2.%J.err
module load trinity/2.6
Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
{{< /highlight >}}
{{% /panel %}}
The third step of running Trinity is to run Trinity with the option **--no_run_butterfly**:
{{% panel header="`trinity_step3.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Trinity_Step3
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Trinity_Step3.%J.out
#SBATCH --error=Trinity_Step3.%J.err
module load trinity/2.6
Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
{{< /highlight >}}
{{% /panel %}}
The fourth step of running Trinity is to run Trinity without any additional option:
{{% panel header="`trinity_step4.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Trinity_Step4
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Trinity_Step4.%J.out
#SBATCH --error=Trinity_Step4.%J.err
module load trinity/2.6
Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
{{< /highlight >}}
{{% /panel %}}
### Trinity Output
Trinity outputs number of files in its `trinity_out/` output directory after each executed step. The output file `Trinity.fasta` is the final Trinity output that contains the assembled transcripts.
{{% notice tip %}}
The Inchworm (step 1) and Chrysalis (step 2) steps can be memory intensive. A basic recommendation is to have **1GB of RAM per 1M ~76 base Illumina paired-end reads**.
{{% /notice %}}
+++
title = "Velvet"
description = "How to use Velvet on HCC machines"
weight = "52"
+++
[Velvet] (https://www.ebi.ac.uk/~zerbino/velvet/) is a general sequence assembler designed to produce assembly from short, as well as long reads. Running Velvet consists of a sequence of two commands **velveth** and **velvetg**. **velveth** produces a hash table of k-mers, while **velvetg** constructs the genome assembly. The k-mer length, also known as hash length corresponds to the length, in base pairs, of the words of the reads being hashed.
Velvet has lots of parameters that can be found in its [manual] (https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf). However, the k-mer value is crucial in obtaining optimal assemblies. Higher k-mer values increase the specificity, and lower k-mer values increase the sensitivity.
Velvet supports multiple file formats: `fasta`, `fastq`, `fasta.gz`, `fastq.gz`, `sam`, `bam`, `eland`, `gerald`. Velvet also supports different read categories for different sequencing technologies and libraries, e.g. `short`, `shortPaired`, `short2`, `shortPaired2`, `long`, `longPaired`.
Each step of Velvet (**velveth** and **velvetg**) may be run as its own job. The following pages describe how to run Velvet in this manner on HCC and provide example submit scripts:
{{% children %}}
### Useful Information
In order to test the Velvet (velvet/1.2) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Velvet on Tusker are shown in the table below:
{{< readfile file="/static/html/velvet.html" >}}
+++
title = "Running Velvet with Paired-End Data"
description = "How to run velvet with paired-end data on HCC resources"
weight = "10"
+++
## Running Velvet with Paired-End long fastq data with k-mer=43, 8 CPUs and 100GB of RAM
The first step of running Velvet is to run **velveth**:
{{% panel header="`velveth.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Velvet_Velveth
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=Velveth.%J.out
#SBATCH --error=Velveth.%J.err
module load velvet/1.2
export OMP_NUM_THREADS=$SLURM_NTASKS_PER_NODE
velveth output_directory/ 43 -fastq -longPaired -separate input_reads_pair_1.fastq input_reads_pair_2.fastq
{{< /highlight >}}
{{% /panel %}}
After running **velveth**, the next step is to run **velvetg** on the `output_directory/` and files generated from **velveth**:
{{% panel header="`velvetg.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --job-name=Velvet_Velvetg
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Velvetg.%J.out
#SBATCH --error=Velvetg.%J.err
module load velvet/1.2
export OMP_NUM_THREADS=$SLURM_NTASKS_PER_NODE
velvetg output_directory/ -min_contig_lgth 200
{{< /highlight >}}
{{% /panel %}}
Both **velveth** and **velvetg** are multi-threaded.
### Velvet Output
{{% panel header="`Output directory after velveth`"%}}
{{< highlight bash >}}
$ ls output_directory/
Log Roadmaps Sequences
{{< /highlight >}}
{{% /panel %}}
{{% panel header="`Output directory after velvetg`"%}}
{{< highlight bash >}}
$ ls output_directory/
contigs.fa Graph LastGraph Log PreGraph Roadmaps Sequences stats.txt
{{< /highlight >}}
{{% /panel %}}
The output fasta file `contigs.fa` is the final Velvet output that contains the assembled contigs. More information about the output files is provided in the Velvet manual.