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.

uBAM output (--output-format ubam)

Emit records as unaligned BAM (uBAM) instead of FASTQ. Useful for pipelines that carry BAM downstream (10X single-cell, methylation callers, anything that wants to preserve BAM aux tags through the trim step).

Input	uBAM output
Single-end	INPUT_trimmed.bam
Paired-end	INPUT_val.bam — one interleaved BAM per pair

Paired output follows the samtools/Picard/fgbio convention: R1 and R2 records interleave in a single BAM with FREAD1 (0x40) / FREAD2 (0x80) flag bits. No separate _val_1.bam / _val_2.bam files.

uBAM output is currently single-threaded — --cores N is ignored for BAM writing; FastQC (when --fastqc is requested) still uses the value.

@PG chain preservation

The input @HD / @PG header chain is propagated verbatim, and a trim_galore @PG line is appended:

@PG  ID:trim_galore  VN:<version>  CL:<command-line>

uBAM-in → uBAM-out is therefore not byte-identical to the input — provenance is preserved by adding to history, same treatment as samtools / Picard. The output records themselves round-trip losslessly.

Aux-tag round-trip with --preserve-tags

--preserve-tags TAG1,TAG2,... (samtools -T-compatible, comma-separated) carries listed aux tags from input records through trimming into output records. Supports A / Z / i / f scalar types; array (B) and hex (H) types are rejected because the FASTQ intermediate cannot textually encode them.

Typical uses:

• --preserve-tags CB,UB — 10X cell / UMI barcodes for single-cell
• --preserve-tags RG,LB,BC — read-group and library metadata

FASTQ input silently ignores --preserve-tags (there are no source tags to carry).

Feature compatibility

Most FASTQ-shaped features work with uBAM output. Rejected at CLI-validate time (v1 scope):

• --dont_gzip — gzip flag is FASTQ-output-specific; uBAM is BGZF-framed unconditionally
• --clock, --implicon — specialty modes encode UMI in the FASTQ header, which can't round-trip through the BAM record
• --demux — one output file per barcode; uBAM demux is a planned follow-up
• --passthrough — carrier FASTQ shape is FASTQ-specific
• --retain_unpaired — would produce singleton BAMs; not in v1
• --clumpify — in-place reorder is FASTQ-shape-specific (note: --clump_only --output-format ubam is supported — see Clump-only)

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 output. Works on both FASTQ output (default) and uBAM output (--output-format ubam) — fastqc-rust reads .bam natively, so no intermediate conversion. No Java or external fastqc install needed.

For paired-end runs, FastQC is invoked once per output file — so PE FASTQ produces two reports (one per mate), while PE uBAM produces a single report per pair (uBAM PE output is one interleaved BAM, and the report covers both mates pooled).

--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.