NAME

trim_fastq.pl - Trim sequence and quality string of fastq files on the fly

SYNOPSIS

trim_fastq.pl [-f FILE] [-u INTEGER] [-d INTEGER] [-a5 STRING] [options]

DESCRIPTION

This program trims sequence and qualitystring fields from a fastq file, either by a number of nucleotides, or by removing a user defined 5' adapter sequence. The typical usage scenario is to allow re-mapping if mapping quality is not sufficient without trimming.

OPTIONS

--fastq -f

Fastq file for trimming

--up -u

Number of nucleotides to trim from read / quality string start

--down -d

Number of nucleotides to trim from read / quality string end

--a5

Sequence of 5' adapter to trim from the left side of the reads. This option and -u / -d are mutually exclusive

--help -h

Print short help

--man

Prints the manual page and exits

AUTHORS

Joerg Fallmann <joerg.fallmann@univie.ac.at> Michael T. Wolfinger <michael@wolfinger.eu>