.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH FASTQ-CLIPPER "1" "July 2015" "fastq-clipper 1.1.2" "User Commands"
.SH NAME
fastq-clipper \- ea-utils: removes one or more adapter sequences from the fastq file
.SH DESCRIPTION
usage: fastq\-clipper [options] <fastq\-file> <adapters>
.PP
Removes one or more adapter sequences from the fastq file.
Adapter sequences are colon\-delimited.
Stats go to stderr, unless \fB\-o\fR is specified.
.SH OPTIONS
.TP
\fB\-h\fR
This help
.TP
\fB\-o\fR FIL
Output file (stats to stdout)
.TP
\fB\-p\fR N
Maximum difference percentage (10)
.TP
\fB\-m\fR N
Minimum clip length (1)
.TP
\fB\-l\fR N
Minimum remaining sequence length (15)
.TP
\fB\-x\fR [N]
Extra match length past adapter length,
.IP
N =\-1 : search all
N = 0 : search only up to adapter length
.TP
\fB\-e\fR
End\-of\-line (default)
.TP
\fB\-b\fR
Beginning\-of\-line (not supported yet)