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

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.

Build Status install with bioconda container ready

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/0.4.5.tar.gz -o trim_galore.tar.gz
tar xvzf trim_galore.tar.gz
# Run Trim Galore
~/TrimGalore-0.4.5/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