Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff.

Trim Galore! can remove sequences if they become too short during the trimming process.The Phred quality of basecalls and the stringency for adapter removal can be specified individually.For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming.This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps.

For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too.You are invited to leave comments, feature request or bug reports over there! Trim Galore is now also available from GitHub. Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.Ī functional version of Cutadapt and optionally FastQC are required.

Trimmomatic crop example