Trim Galore

note

Quality and adapter trimming for next-generation sequencing data, with special handling for RRBS libraries.

https://github.com/FelixKrueger/TrimGalore

Trim Galore provides consistent quality and adapter trimming for next-generation sequencing data, with special handling for Reduced Representation Bisulfite Sequencing (RRBS) and small-RNA libraries.

This MultiQC module supports Trim Galore v2.0, which is a Rust rewrite of the original Perl-based v0.6 that has a new JSON output file summarising results. The earlier v0.6 versions of Trim Galore that wrapped Cutadapt are supported with reporting via the Cutadapt module. The old log format is still produced, but the Cutadapt module search pattern is configured to skip reports mentioning Trim Galore v2+. If you delete the JSON but keep the v2 text file, the sample will not be reported by either module.

Paired-end sample grouping

R1 and R2 of a paired-end sample are grouped automatically into a single row in the General Statistics and Pair Validation tables. Click the expand arrow on a grouped row to see the per-read values. The grouping is derived from the file list inside each JSON report, so it does not depend on filename patterns.

To disable automatic grouping and show one row per read everywhere:

trim_galore_config:
  auto_group_pairs: false

Auto-grouping can be combined with the global table_sample_merge config option to merge further — for example to group lanes of an already-paired sample.

File search patterns

trim_galore:
  fn: '*_trimming_report.json'