Trim galore

Trim Galore is a versatile tool for trimming sequencing reads and removing adapter sequences. It’s particularly useful for preparing raw sequencing data for downstream applications like alignment or differential expression/methylation analysis. Trim Galore combines the functionalities of Cutadapt and FastQC for quality control and trimming.

trim_galore --paired --cores $task.cpus $args $reads

Common Options

• -q <quality>: Trim low-quality bases from the ends of reads. Default is 20.

• --length <min_length>: Discard reads shorter than the specified length after trimming.

• --adapter <sequence>: Specify a custom adapter sequence. By default, Trim Galore auto-detects adapters.

• --gzip: Compress the output files into .gz format.

• --fastqc: Run FastQC before and after trimming.

• --cores <number>: Use multiple cores for faster processing.