For removing contaminant adapters and read quality trimming

Internally based on tools Cutadapt and FastQC

Install "Trim Galore"

(a) using a conda environment

conda install -c bioconda trim-galore

https://anaconda.org/bioconda/trim-galore

(b) direct install from GitHub

# requires separate installation of Cutadapt and FastQC

https://github.com/FelixKrueger/TrimGalore

Run "Trim Galore" on paired-read samples

# adapter removal and read quality trimming of paired-read fastq-files

trim_galore --paired SAMPLE_R1.fastq.gz SAMPLE_R2.fastq.gz

Documentation

https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md