SOAP has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis. Currently, it consists of several programs:
SOAP3 SOAP2 SOAPsnp SOAPsv SOAPfuse SOAP-PopIndel SOAPindel SOAPHla SOAPsplice SOAPdenovo SOAPals SOAPfusion SOAPsnp
A GPU-accelerated alignment tool called SOAP3 is also available on Biowulf. (SOAP3 on Biowulf)
All the SOAP packages are installed in /usr/local/apps/soap/. The command 'module load soap' will add the latest version of each package executables to your path. Versions of each package can be seen with the 'module show soap' command.
1. Create a script file. The file will contain the lines similar to the lines below.
#!/bin/bash # This file is soapScript # #PBS -N soap #PBS -m be #PBS -k oe module load soap cd /data/user/soap/run1 # align single-end reads with soap, using 16 threads soap -a reads_a -D index_files -o output -n 16 # align paired-end reads and detect splice junctions with soapsplice, 16 threads soapsplice -d 2BWT_INDEX_PREFIX -l reads_a -r length_of_reads -I insert_length -o output_prefix -p 16 # diploid genome resequencing soapsnp -i
-d -o -r 0.00005 -e 0.0001 -t -u -L -M
2. Submit the script using the 'qsub' command on Biowulf.
$ qsub -l nodes=1:x2800 ./script
Note: here 'x2800' was specified which means the job will be running on one 'x2800' node. Depending on the number of threads specified and the amount of memory required, different types of nodes can be specified instead of x2800. Run 'freen' to check for current availabe node types and numbers.
User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node.
First set the paths using 'module load soap'. Allocate an interactive node as described below, and run the interactive job there.
biowulf% qsub -I -l nodes=1:g24:c16 qsub: waiting for job 2236960.biobos to start qsub: job 2236960.biobos ready [user@p2013]$ module load soap [user@p2013]$ cd /data/user/myruns [user@p2013]$ soap -a reads_a -D index_files -o output -n 16 [user@p2013]$ soapsplice -d 2BWT_INDEX_PREFIX -l reads_a -r length_of_reads -I insert_length -o output_prefix -p 16 [user@p2013]$ exit qsub: job 2236960.biobos completed