trim

The trim command trims FASTQ sequences from the 3’ end when quality drops below a threshold in a sliding window.

Usage

seqfu trim [options] [<inputfile> ...]

Options

Option	Description	Default
-w, --window-size INT	Window size for quality calculation	5
-q, --min-avg-qual INT	Minimum average quality within window	20
--offset INT	Quality offset (33 for Illumina)	33
-o, --output FILE	Output filename	stdout
-v, --verbose	Verbose output	off
-h, --help	Show help

Description

This command scans the quality scores of FASTQ sequences using a sliding window of the specified size. When the average quality within the window drops below the specified threshold, it trims the sequence from that position, discarding all subsequent bases.

This is useful for removing low-quality regions from the 3’ end of sequencing reads, which often contain more errors as the sequencing reaction progresses.

Examples

Trim sequences when the quality drops below 20 in a window of 5 bases:

seqfu trim input.fastq -o output.fastq

Use a more stringent quality threshold:

seqfu trim -q 25 input.fastq -o output.fastq

Change the window size:

seqfu trim -w 10 -q 20 input.fastq -o output.fastq