TrimFastq

Overview

Group: FASTQ

Trims reads in one or more line-matched fastq files to a specific read length. The individual fastq files are expected to have the same set of reads, as would be the case with an r1.fastq and r2.fastq file for the same sample.

Optionally supports dropping of reads across all files when one or more reads is already shorter than the desired trim length.

Input and output fastq files may be gzipped.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToFastq	One or more input fastq files.	Required	Unlimited
output	o	PathToFastq	A matching number of output fastq files.	Required	Unlimited
length	l	Int	Length to trim reads to (either one per input fastq file, or one for all).	Required	Unlimited
exclude	x	Boolean	Exclude reads below the trim length.	Optional	1	false