Output files

Trim Galore writes one trimmed FASTQ per input, plus a per-input text and JSON trimming report. File naming matches v0.6.x exactly, so existing pipelines continue to work without changes.

Single-end

File	Contents
INPUT_trimmed.fq.gz	Trimmed reads.
INPUT_trimming_report.txt	Cutadapt-compatible text report.
INPUT_trimming_report.json	Structured JSON report (schema v1, for MultiQC).

INPUT is the original filename minus the .fastq / .fq (and .gz) suffix.

Paired-end

File	Contents
R1_val_1.fq.gz	Validated Read 1, post-trim and post-pair-validation.
R2_val_2.fq.gz	Validated Read 2.
R1.fastq.gz_trimming_report.txt / .json	Read 1 report.
R2.fastq.gz_trimming_report.txt / .json	Read 2 report. Carries the final pair counts.

Singleton (unpaired) reads

With --retain_unpaired:

File	Contents
R1_unpaired_1.fq.gz	Read 1 reads whose mate dropped below --length_2.
R2_unpaired_2.fq.gz	Read 2 reads whose mate dropped below --length_1.

Specialty modes

Specialty modes write to mode-specific filenames and exit before the main pipeline:

Mode	Output
--hardtrim5 N	*.{N}bp_5prime.fq(.gz)
--hardtrim3 N	*.{N}bp_3prime.fq(.gz)
--clock	*.clock_UMI.R1.fq(.gz) / *.clock_UMI.R2.fq(.gz)
--implicon[=N]	*_{N}bp_UMI_R1.fastq(.gz) / *_{N}bp_UMI_R2.fastq(.gz)
--demux	One file per barcode (single-end input only).

Compression

Gzip-compressed input produces gzip-compressed output by default. Pass --dont_gzip to write plain FASTQ.

Output directory

--output_dir DIR writes outputs to DIR/ instead of the current working directory. The trimmed FASTQ filename stem is unchanged; only the parent directory differs.

Renaming outputs

--rename PREFIX replaces the input filename stem in the output names. Useful for pipelines that thread sample IDs through trimming separately from input filenames.

FastQC

--fastqc runs the bundled fastqc-rust library on the trimmed output files after pair validation, producing FastQC 0.12.1-compatible HTML + ZIP reports alongside the trimmed FASTQ. No Java or external fastqc install needed.

--fastqc_args "..." passes a subset of FastQC flags through. Currently supported: --nogroup, --expgroup, --quiet, --svg, --nano, --nofilter, --casava, -t/--threads, -o/--outdir. Other flags emit a warning and are ignored.