The trim command provides comprehensive quality trimming and filtering for FASTQ files, with an interface and efficiency similar to fastp. It supports both single-end and paired-end reads.

By default, it performs 3’ sliding window trimming and quality filtering.

Usage

For single-end reads:

seqfu trim [options] <input.fq>

For paired-end reads:

seqfu trim [options] -1 <R1.fq> [-2 <R2.fq>]

Options

Input Options

Option	Description	Default
<input>	Single-end FASTQ file. Use - for stdin.
-1, --r1 FILE	R1 file for paired-end reads.
-2, --r2 FILE	R2 file for paired-end reads. If not specified, it’s auto-detected based on the R1 filename.
--for-tag TAG	Pattern for R1 files for auto-detection.	auto
--rev-tag TAG	Pattern for R2 files for auto-detection.	auto

Output Options

Option	Description	Default
-o, --output FILE/BASE	Output file for single-end, or output basename for paired-end (required for PE).	stdout
--r1-suffix SUFFIX	Suffix for the R1 output file in paired-end mode.	_R1.fastq
--r2-suffix SUFFIX	Suffix for the R2 output file in paired-end mode.	_R2.fastq
-z, --compress	Compress output with gzip. Paired output names gain .gz unless already present.	off

Fixed Position Trimming

Option	Description	Default
--trim-front N	Trim N bases from the 5’ end of each read.	0
--trim-tail N	Trim N bases from the 3’ end of each read.	0

Sliding Window Trimming

This is used to remove low-quality ends of reads.

Option	Description	Default
-5, --cut-front	Enable 5’ sliding window trimming.	off
--no-cut-front	Explicitly disable 5’ sliding window trimming.
--cut-front-window N	Window size for 5’ trimming.	4
--cut-front-qual N	Quality threshold for 5’ trimming.	20
-3, --cut-tail	Enable 3’ sliding window trimming.	on
--no-cut-tail	Disable the default 3’ sliding window trimming.
--cut-tail-window N	Window size for 3’ trimming.	4
--cut-tail-qual N	Quality threshold for 3’ trimming.	20
-r, --cut-right	Enable right-side sliding window trimming (takes precedence over cut-tail).	off
--cut-right-window N	Window size for right-side trimming.	4
--cut-right-qual N	Quality threshold for right-side trimming.	20

Quality Filtering

Enabled by default.

Option	Description	Default
-Q, --disable-quality	Disable all quality filtering.	off
--qualified-qual N	A base is considered qualified if its quality is >= N.	15
--unqualified-percent N	Maximum allowed percentage of unqualified bases per read.	40.0
--avg-qual N	Minimum average quality for a read. Disabled if 0.	0

Other Filtering

Option	Description	Default
-n, --n-base-limit N	Maximum number of N bases allowed in a read.	5
-l, --min-length N	Minimum read length to keep a read.	15
--max-length N	Maximum read length. Disabled if 0.	0
--complexity	Enable low complexity filter.	off
--complexity-threshold F	Minimum complexity ratio (0 to 1).	0.3

Performance

Option	Description	Default
-t, --threads N	Number of threads to use.	1
--batch-size N	Number of reads to process in each batch per thread.	10000

Other Options

Option	Description	Default
--offset N	Quality score offset.	33
--preset PRESET	Apply a preset configuration (strict or lenient).
-v, --verbose	Print verbose statistics to stderr.	off
--stats-json FILE	Write detailed statistics in JSON format to a file.
-h, --help	Show the help message.

Description

The trim command is a versatile tool for cleaning FASTQ data. It can handle both single-end and paired-end reads and offers a wide range of options for trimming and filtering.

By default, seqfu trim enables 3’ tail trimming (--cut-tail) and quality filtering (based on --qualified-qual and --unqualified-percent). Front trimming composes with the default tail trim; use --no-cut-tail for front-only trimming. For paired-end data, both reads must pass all filtering steps to be included in the output.

Presets

Two presets are available for convenience:

• strict: Enables aggressive filtering. Equivalent to --cut-right -l 50 --avg-qual 25.
• lenient: Enables light filtering. Equivalent to --cut-tail -l 30 -Q (disables quality filtering).

Examples

Basic trimming (defaults)

For a single-end file, this uses the default settings: 3’ tail trimming and quality filtering.

seqfu trim input.fq -o output.fq

Paired-end trimming

The R2 file is auto-detected from the R1 name. The output files will be trimmed_R1.fastq and trimmed_R2.fastq.

seqfu trim -1 sample_R1.fq -o trimmed

Aggressive filtering

This example uses the --cut-right method, sets a minimum average quality of 25, and a minimum length of 50 bp.

seqfu trim -1 R1.fq -2 R2.fq -o out --cut-right --avg-qual 25 -l 50

Minimal processing

This disables quality filtering and the default sliding-window tail trim, then applies fixed trimming from both ends.

seqfu trim input.fq -o output.fq -Q --no-cut-tail --trim-front 5 --trim-tail 5