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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 (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 Rust rewrite 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

The repository ships a CITATION.cff file — GitHub's "Cite this repository" button on the repo sidebar generates BibTeX / APA from it.

Trim Galore is archived on Zenodo:

For older versions, pick the version-specific DOI from the corresponding entry on the Zenodo concept page or from the GitHub release page.

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.