.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH FASTQ-JOIN "1" "July 2015" "fastq-join 1.1.2" "User Commands"
.SH NAME
fastq-join \- ea-utils: join two paired-end reads on the overlapping ends
.SH SYNOPSIS
.B fastq-join
[\fI\,options\/\fR] \fI\,<read1.fq> <read2.fq> \/\fR[\fI\,mate.fq\/\fR] \fI\,-o <read.%.fq>\/\fR
.SH DESCRIPTION
fastq\-join: invalid option \fB\-\-\fR 'h'
Unknown option `\-h'.
.PP
Joins two paired\-end reads on the overlapping ends.
.SH OPTIONS
\fB\-o\fR FIL     See 'Output' below
\fB\-v\fR C       Verifies that the 2 files probe id's match up to char C
.IP
use ' ' (space) for Illumina reads
.PP
\fB\-p\fR N       N\-percent maximum difference (8)
\fB\-m\fR N       N\-minimum overlap (6)
\fB\-r\fR FIL     Verbose stitch length report
\fB\-R\fR         No reverse complement
\fB\-x\fR         Allow insert < read length
.PP
Output:
.IP
You can supply 3 \fB\-o\fR arguments, for un1, un2, join files, or one
.PP
argument as a file name template.  The suffix 'un1, un2, or join' is
appended to the file, or they replace a %\-character if present.
.IP
If a 'mate' input file is present (barcode read), then the files
.PP
\&'un3' and 'join2' are also created.