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 default 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 of 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