Installer trim-galore avec Homebrew, apt

Liens du projet

• Page d'accueil

Commandes et alias

• trim_galore

Historique du projet

The original Trim Galore project was developed at Babraham Bioinformatics by Felix Krueger. Official Babraham documentation describes it as a wrapper around Cutadapt and FastQC for consistent quality and adapter trimming of FastQ files, including special handling for MspI-digested RRBS libraries.

The official Trim Galore documentation describes v2.x as a faithful Rust rewrite of the earlier v0.6.x Perl tool. The rewrite consolidated adapter trimming, gzip handling, and FastQC-compatible reporting into a single static binary while retaining compatibility with common v0.6.x scripts and pipelines.

Historique d'adoption

Trim Galore became common in next-generation sequencing preprocessing because it wrapped the separate Cutadapt and FastQC steps behind one stable CLI and produced conventional FASTQ outputs plus trimming reports. The current docs describe more than ten years of production use and identify the older Perl wrapper as a de-facto standard in many bisulfite sequencing pipelines.

Package-manager adoption spans bioinformatics and general Unix packaging channels: the supplied package facts list Homebrew, Debian, and Ubuntu package names, while the official installation guide documents Bioconda, crates.io, Docker, source builds, and prebuilt binaries as current installation paths.

Modes d'utilisation

Typical usage is file-oriented and pipeline-friendly: run `trim_galore input.fastq.gz` for single-end reads, `trim_galore --paired sample_R1.fastq.gz sample_R2.fastq.gz` for paired-end reads, and add workflow-specific flags such as `--rrbs`, `--fastqc`, `--cores`, `--poly_a`, or explicit adapter specifications.

Trim Galore writes trimmed FASTQ files and per-input trimming reports. The v2 documentation also describes structured JSON reports for MultiQC and an in-process FastQC-compatible reporting path.

Pourquoi les passionnés de paquets s'y intéressent

Trim Galore matters to package-manager users because it sits at the boundary between classic scientific scripting and modern single-binary distribution. The old Perl-era package pulled together Perl, Python/Cutadapt, Java/FastQC, and compression tools; the v2 rewrite turns the same familiar CLI into a Rust binary with no runtime dependencies.

For reproducible bioinformatics environments, it is notable that the official install page now supports multiple packaging cultures: Cargo/crates.io, Bioconda, Docker via GitHub Container Registry, source builds, and release binaries, while distro/package-manager metadata in the input shows Homebrew, Debian, and Ubuntu coverage.

Chronologie

• 2012: Official changelog lists v0.1.3 on 14 Mar 2012 and v0.1.4 on 21 Mar 2012.
• 2013: v0.3.x releases expanded the early Perl wrapper line.
• 2019: v0.6.0 was released on 1 Mar 2019.
• 2021: v0.6.7 was released to obtain a Zenodo DOI.
• 2026: v0.6.11 was released on 24 Feb 2026.
• 2026: v2.x introduced the Rust rewrite as a single static binary and drop-in successor to v0.6.x.

Related projects

• Cutadapt was the adapter-trimming engine wrapped by the historical Perl Trim Galore implementation.
• FastQC provided external quality-control reports in the older workflow; v2 integrates FastQC-compatible reporting through fastqc-rust.
• MultiQC is relevant because Trim Galore reports, including v2 JSON reports, are intended for aggregation in sequencing QC workflows.

Sources

• https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
• https://www.trimgalore.com/
• https://www.trimgalore.com/guide/overview/
• https://www.trimgalore.com/install/
• https://www.trimgalore.com/quickstart/
• https://www.trimgalore.com/reference/changelog/
• https://www.trimgalore.com/reference/credits/
• source_facts.package-manager