Trimming reports

Trimming reports are generated by Trim Galore in a Cutadapt-compatible format so existing MultiQC parsers continue to work unchanged. Users migrating from v0.6.x will recognise the structure: v2.x does the work in a single process rather than interleaving output from a Cutadapt subprocess, but the emitted text still begins with a This is cutadapt ... (compatible; for MultiQC backwards compatibility) banner so downstream tools parse it correctly.

Reports consist of three sections:

1. Parameter summary
2. Cutadapt-compatible trimming summary
3. Run statistics summary

1. Parameter summary

Written out right at the start of the run. Example (paired-end, default options):

SUMMARISING RUN PARAMETERS
==========================
Input filename: SLX_R1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 2.1.0 (Oxidized Edition)
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Illumina adapter for trimming (count: 18772). Second best hit was smallRNA (count: 0)
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file will be GZIP compressed

The parameter summary in v2.x is slightly slimmer than the v0.6.x equivalent: entries like Cutadapt version:, Python version:, the per-core annotation, and FastQC/clip status lines are not emitted. Cutadapt and Python are not subprocesses in v2.x, and clipping is applied silently during trimming rather than logged here.

2. Cutadapt-compatible trimming summary

After the parameter block, Trim Galore emits a MultiQC-compatible summary that downstream parsers familiar with the Perl/Cutadapt output recognise unchanged. The block starts with two header lines that identify the edition:

Trim Galore 2.1.0 (Oxidized Edition) — adapter trimming built in
This is cutadapt 4.0 (compatible; for MultiQC backwards compatibility)
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SLX_R1.fastq.gz
Processing reads on 1 core in single-end mode ...

=== Summary ===

Total reads processed:           1,166,076,593
Reads with adapters:               467,751,243 (40.1%)
Reads written (passing filters): 1,166,076,593 (100.0%)

Total basepairs processed: 174,911,488,950 bp
Quality-trimmed:             674,749,563 bp (0.4%)
Total written (filtered):  172,939,327,763 bp (98.9%)

Note

Reads written (passing filters) always shows 100% in this block: length and N-content filtering happens in a downstream step, not here. The true discard counts appear in the Run statistics summary below. See issue #200 for background.

The per-adapter detail block follows:

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 467751243 times.

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Overview of removed sequences
length  count  expect  max.err  error counts
1  316729650  291519148.2  0  316729650
2  81494061  72879787.1  0  81494061
3  27821736  18219946.8  0  27821736
...
150  3937  17.4  1  102 3835

If multiple adapters were configured (via repeated -a, inline -a " SEQ -a SEQ", or a FASTA file), each gets its own === Adapter N === block.

3. Run statistics summary

Written at the end of the report. For single-end input it is a short block after the adapter details:

RUN STATISTICS FOR INPUT FILE: SE.fastq.gz
=============================================
1000000 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp: 552 (0.1%)

For paired-end input, the validation step that discards under-length pairs runs after both per-file reports are emitted, so:

• The Read 1 report shows only N sequences processed in total (no post-validation stats).
• The Read 2 report carries the final paired-end validation counts at the very end:

RUN STATISTICS FOR INPUT FILE: SLX_R2.fastq.gz
=============================================
1166076593 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 1166076593

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3357967 (0.29%)

It is this number, 3,357,967 (0.29%) at the end of the Read 2 trimming report, that represents the total number of read pairs removed from both Read 1 and Read 2 files because of filtering (min length, max length, or max N).

JSON report

Trim Galore also writes a JSON report (*_trimming_report.json) alongside the text report. It contains the same statistics as the text report in a structured format (schema v1), designed for native parsing by MultiQC. If you're building a custom dashboard or consuming Trim Galore output programmatically, prefer the JSON file.