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trim galore

Credits & license

History

Section titled “History”

Trim Galore was developed at Babraham Bioinformatics by Felix Krueger (now part of Altos Labs). For roughly a decade it shipped as a Perl wrapper around Cutadapt and was the de-facto standard for adapter trimming in many bisulfite sequencing pipelines.

In 2026, Trim Galore was rewritten in Rust as a single static binary, the Oxidized Edition (v2.x). It is a drop-in replacement for v0.6.x with extra capabilities: poly-G auto-detection, a generic poly-A trimmer, per-pair adapter detection, cleaner multi-adapter syntax, and a structured JSON report. See Migrating from v0.6.x for the changes.

Current development is at github.com/FelixKrueger/TrimGalore.

Contributors

Section titled “Contributors”

Trim Galore is maintained by Felix Krueger. The Oxidized Edition has benefitted from contributions and design input from a number of people; the GitHub contributors page tracks the full list. Notable recent contributions:

  • Phil Ewels — bundled FastQC integration via fastqc-rust, docs site infrastructure (Astro/Starlight), GitHub Actions hardening, hero animation polish.
  • Dongze He (@an-altosian) — Phase-1B Perl-parity hunt and Buckberry-scale performance audit. Reported and prototyped the lowercase clip-flag fix (#242), --max_n fraction-mode UX, the gzip-extension and --retain_unpaired Perl-parity fixes (#245), the --clock/--implicon convenience widening (#245-D), the test-coverage gap inventory (#246), CI hardening recommendations (#247), and the Buckberry-scale performance audit (#248) including the gzip-level and single-buffered-write wins landed in v2.1.0-beta.6.

If you've contributed and would like a line here, please open a PR — the list is intentionally curated rather than auto-generated.

Citing Trim Galore

Section titled “Citing Trim Galore”

If you use Trim Galore in published work, cite the project repository:

Krueger, F. Trim Galore! Consistent adapter and quality trimming for FASTQ files. https://github.com/FelixKrueger/TrimGalore

Trim Galore has a Zenodo DOI for archival citation. Pick the version-specific DOI from the release page for the version you used.

License

Section titled “License”

Trim Galore is released under the GNU General Public License v3.0 (GPL-3.0). The full text is in the LICENSE file.

Reporting issues

Section titled “Reporting issues”
  • Bugs and feature requests: GitHub Issues.
  • Beta feedback: open an issue with the beta-feedback label.
  • Security: contact the maintainer privately rather than filing a public issue.
Section titled “Related tools”
  • FastQC. Quality reports for raw and trimmed FASTQ.
  • MultiQC. Aggregates Trim Galore reports (text and JSON) across samples.
  • Bismark. Bisulfite read aligner. The standard downstream step for RRBS workflows.
  • UmiBam. UMI-aware deduplication for Bismark BAM files. Used with --clock and --implicon.
  • Cutadapt. The adapter-trimming engine that the Perl Trim Galore wrapped. v2 has its own built-in adapter trimmer.