Pittsburgh Supercomputing Center 

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communications and data analytics.

SOAPdenovo

SOAPdenovo is a de novo sequence assembler for short reads produced by next-generation sequencing technology.

Installed on blacklight.

Other resources that may be helpful:

 

Running SOAPdenovo

To run SOAPdenovo you must prepare a batch script and submit it with the qsub command. Information about running batch jobs on blacklight is available in the "Running Jobs" section of the blacklight user document.

A sample script for running SOAPdenovo is

#!/bin/bash
#ncpus must be a multiple of 16
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
##PBS -M <your_email_address>
##PBS -m abe

# edit soap2.config to designate location of fasta/fastq input files
source /usr/share/modules/init/bash
module load soapdenovo2/r240

jobid=`echo $PBS_JOBID | cut -f 1 -d '.'`

# the directory you issued the 'qsub' command from
submitdir=$PBS_O_WORKDIR
name=soap2-r240_test.$jobid
config_file=soap2.config
prefix=soap2_19kmer
# do not set nthreads above 32, no matter how many cores you use, as the code will not scale efficiently
nthreads=16
maxkmer=19
covcutoff=5


scratchdir=$SCRATCH/$name
mkdir -p $scratchdir

SOAPdenovo-63mer pregraph -s $submitdir/$config_file -K $maxkmer -p $nthreads -R -d $covcutoff -o $scratchdir/$prefix >& $submitdir/$name.pregraph.out

SOAPdenovo-63mer contig -g $scratchdir/$prefix >& $submitdir/$name.contig.out

# these final steps are only relevant for assemblies that use paired end reads (example data set uses only single reads)
SOAPdenovo-63mer map -s $submitdir/$config_file -g $scratchdir/$prefix -p $nthreads >& $submitdir/$name.map.out

SOAPdenovo-63mer scaff -g $scratchdir/$prefix -F -p $nthreads >& $submitdir/$name.scaff.out

In the batch script themodule loadcommand determines which versions of SOAPdenovo you execute. You can see the available versions of SOAPdenovo by issuing the command

module avail soapdenovo

We recommend that you use the SOAPdenovo2 versions.

The data files used by the sample script are available for download by using the links on the right hand side of this page and in the directory  /brashear/projects/examples/velvet on blacklight.