Index of /examples/bioinformatics/soapdenovo

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] SOAPdenovo.config 09-Mar-2015 00:29 107 [DIR] bambus2/ 18-Jul-2011 21:08 - [DIR] fastq/ 18-Jul-2011 21:09 - [   ] soap_job.qsub 09-Mar-2015 00:40 297 [   ] soap_job_pe.qsub 09-Mar-2015 00:41 349

SOAPdenovo package example

To run SOAPdenovo at the command line:

Warning: This command takes a lot of time - execute on a compute node
scc4% qrsh -P my_project

scc-ba1% module load soapdenovo/2-r240
scc-ba1% SOAPdenovo-63mer all -K 31 -p 1 -s SOAPdenovo.config -o asm


To submit a single processor job, execute command:
scc4% qsub -P my_project soap_job.qsub


To submit a multiprocessor job, execute command:
scc4% qsub -P my_project soap_job_pe.qsub

Manual for SOAPdenovo:
http://soap.genomics.org.cn/soapdenovo.html#comm2