The organisms and their appropriate environmental variables for all genomes and chromosome files, as well as for short read aligned indices are shown on the link below:
is a tool for removing adapter sequences from DNA sequencing data.
Although most of the adapters are located at the 3' end of the
sequencing read, Cutadapt allows multiple adapter removal from both 3'
and 5' ends.
[Cutadapt] (https://cutadapt.readthedocs.io/en/stable/index.html) is a tool for removing adapter sequences from DNA sequencing data. Although most of the adapters are located at the 3' end of the sequencing read, Cutadapt allows multiple adapter removal from both 3' and 5' ends.
where **<adapter\_sequence>** is the nucleotide sequence of the
actual adapter, i**nput\_reads.\[fasta\|fastq\]** is the input file with
sequencing data in fasta/fastq format, and respectively,
**output\_reads.\[fasta\|fastq\]** is the final trimmed file in
fasta/fastq format. The option **-a** allows removing of an adapter from
the 3' end of the sequencing read. The option **-b** removes adapters
ligated to the 5' or 3' end. The option **-g** removes adapter sequences
from the 5' end. These options can be used multiple times for different
adapters.
where **<adapter_sequence>** is the nucleotide sequence of the actual adapter, **input_reads.[fasta|fastq]** is the input file with sequencing data in fasta/fastq format, and respectively, **output_reads.[fasta|fastq]** is the final trimmed file in fasta/fastq format.
\\
The option **-a** allows removal of adapters from the 3' end of the sequencing read. The option **-b** removes adapters ligated to the 5' or 3' end. The option **-g** removes adapter sequences from the 5' end. These options can be used multiple times for different adapters.
More information about the Cutadapt options can be found by typing:
**Additional Cutadapt Options**
``` syntaxhighlighter-pre
[<username>@login.tusker~]$ cutadapt --help
```
Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG**
and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of
single-end fasta input file is shown below:
**cutadapt.submit**
\#!/bin/sh
\#SBATCH --job-name=Cutadapt
\#SBATCH --nodes=1
\#SBATCH --ntasks-per-node=1
\#SBATCH --time=168:00:00
\#SBATCH --mem=30gb
\#SBATCH --output=Cutadapt.%J.out
\#SBATCH --error=Cutadapt.%J.err
| |
|-------------------------------------|
| module load python/2.7 cutadapt/1.4 |
cutadapt -a AGGCACACAGGG -a TGAGACACGCA -g AACCGGTT input\_reads.fasta
> output\_reads.fasta
Cutadapt is single threaded program, and therefore **\#SBATCH
--nodes=1** and **\#SBATCH --ntasks-per-node=1**. Cutadapt allows
paired-end trimming where each pair is trimmed separately in a single
pass:
**Cutadapt Usage for Paired-End Reads**
``` syntaxhighlighter-pre
cutadapt -a ADAPTER_PAIR_1 input_reads_pair_1.fastq > output_reads_pair_1.fastq
cutadapt -a ADAPTER_PAIR_2 input_reads_pair_2.fastq > output_reads_pair_2.fastq
```
**Cutadapt Output**
Beside the fasta/fastq file of reads with removed adapter sequences,
Cutadapt also outputs useful statistics per adapter sequence.
Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG** and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of single-end fasta input file is shown below:
{{% panel header="`cutadapt.submit`"%}}
{{<highlightbash>}}
#!/bin/sh
#SBATCH --job-name=Cutadapt
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=Cutadapt.%J.out
#SBATCH --error=Cutadapt.%J.err
module load cutadapt/1.13
cutadapt -a AGGCACACAGGG -a TGAGACACGCA -g AACCGGTT input_reads.fasta > output_reads.fasta
{{</highlight>}}
{{% /panel %}}
Cutadapt is single threaded program, and therefore `#SBATCH --nodes=1` and `#SBATCH --ntasks-per-node=1`.
\\
\\
\\
Cutadapt allows paired-end trimming where each pair is trimmed separately in a single pass:
{{<highlightbash>}}
$ cutadapt -a ADAPTER_PAIR_1 input_reads_pair_1.fastq > output_reads_pair_1.fastq
$ cutadapt -a ADAPTER_PAIR_2 input_reads_pair_2.fastq > output_reads_pair_2.fastq
is a tool used for filtering, formatting or trimming genome and
metagenomic sequence data in fasta/fastq format. Moreover, PRINSEQ
generates summary statistics of sequence and quality data.
[PRINSEQ (PReprocessing and INformation of SEQuence data)] (http://prinseq.sourceforge.net/) is a tool used for filtering, formatting or trimming genome and metagenomic sequence data in fasta/fastq format. Moreover, PRINSEQ generates summary statistics of sequence and quality data.
More information about the PRINSEQ program can be shown with:
where **input_reads.[fasta|fastq]** is an input file of sequence data in fasta/fastq format, and **options** are additional parameters that can be found in the [PRINSEQ manual] (http://prinseq.sourceforge.net/manual.html).
The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qual), **3** (fastq), **4** (fastq and input fasta), and **5** (fastq, fasta and qual).
Simple PRINSEQ SLURM script for single-end fasta data and fasta output format is shown below:
where **input_reads_pair_1.[fasta|fastq]** and **input_reads_pair_2.[fasta|fastq]** are pair 1 and pair 2 of the input files of sequence data in fasta/fastq format, and **options** are additional parameters that can be found in the the [PRINSEQ manual] (http://prinseq.sourceforge.net/manual.html).
PRINSEQ is single threaded program, and therefore both **\#SBATCH
--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
**
**
The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qual), **3** (fastq), **4** (fastq and input fasta), and **5** (fastq, fasta and qual).
**PRINSEQ Output**
Simple PRINSEQ SLURM script for paired-end fastq data and fastq output format is shown below:
{{% panel header="`prinseq_paired_end.submit`"%}}
{{<highlightbash>}}
#!/bin/sh
#SBATCH --job-name=PRINSEQ
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=PRINSEQ_paired.%J.out
#SBATCH --error=PRINSEQ_paired.%J.err
PRINSEQ gives statistics about the input and filtered sequences, and
also outputs single-end or paired-end files of sequences filtered by
PRINSEQ gives statistics about the input and filtered sequences, and also outputs files of single-end or paired-end sequences filtered by specified parameters.
is a 3' end adapter trimmer that uses a Naive Bayesian approach to
classify contaminant substrings in sequence reads. 3' ends often include
poor quality bases which need to be removed prior the quality-based
trimming, mapping, assemblies, and further analysis.
[Scythe] (https://github.com/vsbuffalo/scythe) is a 3' end adapter trimmer that uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. 3' ends often include poor quality bases which need to be removed prior the quality-based trimming, mapping, assemblies, and further analysis.
The basic usage of Scythe is:
{{<highlightbash>}}
$ scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
{{</highlight>}}
where **adapter_file.fasta** is fasta input file of the adapter sequences that need to be removed from the 3' end of the sequence data, and **input_reads.fastq** is the input sequencing data in fastq format.
**General Scythe Usage**
``` syntaxhighlighter-pre
scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
```
where **adapter\_file.fasta** is a fasta input file of the adapter
sequences that need to be removed from the 3' end of the sequence data,
and **input\_reads.fastq** is the input sequencing data in fastq format.
The file **output\_reads.fastq** contains the sequencing reads with
removed adapters. If the adapter sequences are unknown, Scythe by itself
provides two adapter sequences that can be used with the **-a**
option: **illumina\_adapters.fa** and **truseq\_adapters.fasta**.
The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides two adapter sequences that can be used with the **-a** option: **illumina_adapters.fa** and **truseq_adapters.fasta**.
More information about Scythe can found by typing:
**Additional Scythe Options**
``` syntaxhighlighter-pre
[<username>@login.tusker ~]$ scythe --help
```
Simple Scythe script that uses the **illumina\_adapters.fa** file and
**input\_reads.fastq** for Tusker is shown below:
**scythe.submit**
\#!/bin/sh
\#SBATCH --job-name=Scythe
\#SBATCH --nodes=1
\#SBATCH --ntasks-per-node=1
\#SBATCH --time=168:00:00
\#SBATCH --mem=20gb
\#SBATCH --output=Scythe.%J.out
\#SBATCH --error=Scythe.%J.err
| |
|--------------------------|
| module load scythe/0.991 |
scythe -a $SCYTHE\_HOME/illumina\_adapters.fa input\_reads.fastq -o
output\_reads.fastq
Scythe is single threaded program, and therefore both **\#SBATCH
--nodes** and **\#SBATCH --ntasks-per-node** are set to **1**. The two
adapter sequences provided by Scythe are stored in **$SCYTHE\_HOME**.
Hence, to access the illumina adapter file
use: **$SCYTHE\_HOME/illumina\_adapters.fa**, and to access the TruSeq
Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.fastq` for Tusker is shown below:
{{% panel header="`scythe.submit`"%}}
{{<highlightbash>}}
#!/bin/sh
#SBATCH --job-name=Scythe
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=Scythe.%J.out
#SBATCH --error=Scythe.%J.err
module load scythe/0.991
scythe -a ${SCYTHE_HOME}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
{{</highlight>}}
{{% /panel %}}
Scythe is single threaded program, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` are set to **1**.
The two adapter sequences provided by Scythe are stored in **$SCYTHE_HOME**. Hence, to access the illumina adapter file use: `$SCYTHE_HOME/illumina_adapters.fa`, and to access the TruSeq file use: `$SCYTHE_HOME/truseq_adapters.fasta`.
