caitlingilbert / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Trim Galore

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

Installation

Trim Galore is a a Perl wrapper around two tools: Cutadapt and FastQC. To use, ensure that these two pieces of software are available and copy the trim_galore script to a location available on the PATH.

For example:

# Check that cutadapt is installed
cutadapt --version
# Check that FastQC is installed
fastqc -v
# Install Trim Galore
curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.0.tar.gz -o trim_galore.tar.gz
tar xvzf trim_galore.tar.gz
# Run Trim Galore
~/TrimGalore-0.6.0/trim_galore

Documentation

For instructions on how to use Trim Galore, please see the User Guide.

Credits

Trim Galore was developed at The Babraham Institute by @FelixKrueger. You can find it's project page here: bioinformatics.babraham.ac.uk