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Trim Galore

Trim Galore is a wrapper script to automate quality and adaptor trimming as well as quality control, with functionality to remove biased methylation positions for Reduced Representation Bisufite-Seq sequence files.

Trim Galore is available as a module on Apocrita.

Usage

To run the latest installed version of Trim Galore, simply load the trimgalore module:

module load trimgalore

For usage documentation, run trim_galore -h.

Cutadapt dependency

Trim Galore requires Cutadapt as a dependency to run, which can be installed inside a python virtual environment.

Example job

Serial job

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

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

module load trimgalore

trim_galore input.fastq \
            --fastqc \
            --fastqc_args '--nogroup --outdir outdir' \
            --output_dir outdir

References