soapdenovo2.md

+++
title = "SOAPdenovo2"
description =  "How to run SOAPdenovo2 on HCC resources"
weight = "10"
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[SOAPdenovo](http://soap.genomics.org.cn/soapdenovo.html) is a de novo genome assembler for short reads. It is specially designed for Illumina GA short reads and large plant and animal genomes. SOAPdenovo2 is a newer version of SOAPdenovo with improved algorithm that reduces memory consumption, resolves more repeat regions, increases coverage, and optimizes the assembly for large genomes.

SOAPdenovo2 has two commands, **SOAPdenovo-63mer** and **SOAPdenovo-127mer**. The first one is suitable for assembly with k-mer values less than 63 bp, requires less memory and runs faster. The latter one works for k-mer values less than 127 bp.


In order to see the options available for **SOAPdenovo-63mer** just
type:
{{< highlight bash >}}
$ SOAPdenovo-63mer
{{< /highlight >}}

SOAPdenovo2 provides a mechanism to run the whole workflow at once, or in 5 separate steps.


The basic usage of SOAPdenovo2 is:
{{< highlight bash >}}
$ SOAPdenovo-63mer all -s configFile -o output_directory/outputGraph -K <kmer_value> [options]
{{< /highlight >}}
where **configFile** is a defined configuration file, **outputGraph** is the prefix of the output files, and **kmer_value** is the value of k-mer used for building the assembly (`<=63` for SOAPdenovo-63mer and `<=127` for SOAPdenovo-127mer).


If you want to run the assembly process step by step, then use the following sequential commands:

{{% panel theme="info" header="SOAPdenovo2 Step 1 Options" %}}
{{< highlight bash >}}
SOAPdenovo-63mer pregraph -s configFile -o outputGraph [options]
OR
SOAPdenovo-63mer sparse_pregraph -s configFile -K <kmer_value> -z <genome_size> -o outputGraph [options]
{{< /highlight >}}
{{% /panel %}}

{{% panel theme="info" header="SOAPdenovo2 Step 2 Options" %}}
{{< highlight bash >}}
SOAPdenovo-63mer contig -g inputGraph [options]
{{< /highlight >}}
{{% /panel %}}

{{% panel theme="info" header="SOAPdenovo2 Step 3 Options" %}}
{{< highlight bash >}}
SOAPdenovo-63mer map -s configFile -g inputGraph [options]
{{< /highlight >}}
{{% /panel %}}

{{% panel theme="info" header="SOAPdenovo2 Step 4 Options" %}}
{{< highlight bash >}}
SOAPdenovo-63mer scaff -g inputGraph [options]
{{< /highlight >}}
{{% /panel %}}

As you can notice from the commands above, in order to run SOAPdenovo2, you first need to create a config file (`configFile`) that contains different information about the read files (`read length`, `insert size`, `reads location`). SOAPdenovo2 accepts read files in 3 formats: fasta, fastq and bam.


The example configuration file **configFile** for 2 paired-end fastq files, 1 paired-end fasta file and 1 single-end fastq file looks like:
{{% panel header="`configFile`"%}}
{{< highlight bash >}}
#maximal read length
max_rd_len=150
[LIB]
#average insert size of the library
avg_ins=300
#if sequences are forward-reverse of reverse-forward
reverse_seq=0
#in which part(s) the reads are used (only contigs, only scaffolds, both contigs and scaffolds, only gap closure)
asm_flags=3
#cut the reads to the given length
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#paired-end fastq files, read 1 file should always be followed by read 2 file
q1=input_reads1_pair_1.fq
q2=input_reads1_pair_2.fq
#another pair of paired-end fastq files, read 1 file should always be followed by read 2 file
q1=input_reads2_pair_1.fq
q2=input_reads2_pair_2.fq
#paired-end fasta files, read 1 file should always be followed by read 2 file
f1=input_reads_pair_1.fa
f2=input_reads_pair_2.fa
#fastq file for single reads
q=input_reads.fq
{{< /highlight >}}
{{% /panel %}}

After creating the configuration file **configFile**, the next step is to run the assembler using this file.


Simple SLURM script for running SOAPdenovo2 with `k-mer=31`, `8 CPUSs` and `50GB of RAM` is shown below:
{{% panel header="`soapdenovo2.submit`"%}}
{{< highlight bash >}}
#!/bin/bash
#SBATCH --job-name=SOAPdenovo2
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=50gb
#SBATCH --output=SOAPdenovo2.%J.out
#SBATCH --error=SOAPdenovo2.%J.err

module load soapdenovo2/r240

SOAPdenovo-63mer all -s configFile -K 31 -o output_directory/output31 -p $SLURM_NTASKS_PER_NODE
{{< /highlight >}}
{{% /panel %}}


### SOAPdenovo2 Output

SOAPdenovo2 outputs number of files in its `output_directory/` after each executed step. The final assembly output is in the `.contig` file.
{{% panel header="`Output directory after SOAPdenovo2`"%}}
{{< highlight bash >}}
$ ls
output31.Arc            output31.ContigIndex       output31.gapSeq    output31.newContigInde
output31.bubbleInScaff  output31.contigPosInscaff  output31.kmerFreq  output31.peGrads
output31.contig         output31.edge.gz           output31.links     output31.preArc
{{< /highlight >}}
{{% /panel %}}


### Useful Information

In order to test the SOAPdenovo2 (soapdenovo2/r240) performance, we used three different size input files. Some statistics about the input files and the time and memory resources used by SOAPdenovo2 are shown in the table below:
{{< readfile file="/static/html/soapdenovo2.html" >}}

In general, SOAPdenovo2 is a memory intensive assembler that requires approximately 30-60 GB memory for assembling 50 million reads. However, SOAPdenovo2 is a fast assembler and it takes around an hour to assemble 50 million reads.