How Trim Galore works

Trim Galore reads FASTQ, applies quality and adapter trimming in a single pass, filters short reads, and writes trimmed FASTQ plus a per-input report. Specialty modes (RRBS, hard-trim, IMPLICON preprocessing, demultiplexing) layer on top. The pipeline is the same for any base-space high-throughput data; bisulfite/RRBS users should also read Bisulfite & RRBS for library-specific guidance.

Adaptive quality and adapter trimming with Trim Galore

Trim Galore handles quality trimming, adapter detection, adapter removal, length filtering, and specialty modes in a single pass over the data, with optional post-trimming quality reporting via the bundled fastqc-rust library (FastQC 0.12.1-compatible HTML + ZIP, no Java required). Originally a Perl wrapper around Cutadapt and an external FastQC install, v2.x is a faithful Rust rewrite that consolidates those passes while preserving the CLI and output filename conventions.

Note

The Oxidized Edition (v2.x) is a faithful Rust rewrite designed as a drop-in replacement for v0.6.x. All of the trimming steps below happen in a single pass over the data rather than as sequential Cutadapt invocations. Outputs match v0.6.x for the core feature set; newer capabilities (e.g. --poly_g auto-detection, a generic --poly_a trimmer) extend beyond the Perl version.

The pipeline runs in this order:

1. Quality trimming. Phred-based, from the 3' end (BWA algorithm).
2. Adapter trimming. Auto-detection or manual sequence; semi-global alignment with a configurable error rate and overlap.
3. RRBS-specific trimming (only with --rrbs). Removes 2 bp from adapter-trimmed reads at MspI sites. See the RRBS mode page.
4. Length filtering. Drops reads (or read pairs) below the cutoff.
5. Paired-end validation. Discards pairs where at least one read became too short.
6. Optional demultiplexing and FastQC.

Specialty modes (--hardtrim5, --hardtrim3, --clock, --implicon) run their own short-circuit pipeline and exit before quality and adapter trimming.

Where to go next

• New to Trim Galore? Start with Quick start.
• Want to know what a flag does or how it interacts with another? See Flag reference notes.
• Working with bisulfite or RRBS? Read Bisulfite & RRBS before tweaking flags.
• Looking up output files and the report format? See Output files and Trimming reports.