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.
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/0.6.10.tar.gz -o trim_galore.tar.gz
tar xvzf trim_galore.tar.gz
# Run Trim Galore
~/TrimGalore-0.6.10/trim_galoreIf you are using Bioconda:
conda install trim-galore
For instructions on how to use Trim Galore, please see the User Guide.
Trim Galore was developed at The Babraham Institute by @FelixKrueger, now part of Altos Labs.