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Skewer

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing paired-end sequences.

Skewer is available as a module on Apocrita.

Usage

To run the latest installed version of Skewer, simply load the skewer module:

$ module load skewer

$ skewer --help
Skewer (A fast and accurate adapter trimmer for paired-end reads)

USAGE: skewer [options] <reads.fastq> [paired-reads.fastq]
    or skewer [options] - (for input from STDIN)

For usage documentation, run skewer --help.

Example job

Serial job

Here is an example job running on 1 core and 1GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load skewer
skewer -t ${NSLOTS} \
       reads1.fastq

Reference