sickle

Overview

sickle – A windowed adaptive trimming tool for FASTQ files using quality

Version 1.33 is installed on the CSF.

Restrictions on use

Details of the licence, restrictions, links to licence docs etc

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/sickle/1.33

Running the application

Please do not run sickle 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

sickle arg1 arg2 > out.log

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Given an example parallel jobscript, including suitable PE

Further info

• sickle website

Updates

None.