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pandaseq
Overview
pandaseq is a program to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases.
Version 2.8 is installed on the CSF.
Restrictions on use
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/pandaseq/2.8
Running the application
Please do not run pandaseq on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings pandaseq arg1 arg2 > out.log
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores. 2-24 permitted. Runs on a single compute node. # $NSLOTS is automatically set to the number of cores requested above pandaseq -T $NSLOTS arg1 arg2 > out.log
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.