.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH NXTRIM "1" "April 2021" "nxtrim 0.4.3" "User Commands"
.SH NAME
nxtrim \- <short_description>
.SH SYNOPSIS
.B nxtrim
\fI\,-1 R1.fastq.gz -2 R2.fastq.gz \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
Program:        nxtrim
Version:        v0.4.3
Contact:        joconnell@illumina.com
.SH COPYRIGHT
Copyright \(co 2016, Illumina, Inc. All rights reserved. See LICENSE for further details.
.SS "Required arguments:"
.TP
\fB\-1\fR [ \fB\-\-r1\fR ] arg
read 1 in fastq format (gzip allowed)
.TP
\fB\-2\fR [ \fB\-\-r2\fR ] arg
read 2 in fastq format (gzip allowed)
.SS "Allowed options:"
.TP
\fB\-O\fR [ \fB\-\-output\-prefix\fR ] arg
output prefix
.TP
\fB\-\-justmp\fR
just creates a the mp/unknown libraries (reads with adapter at the start will be completely N masked)
.TP
\fB\-\-stdout\fR
print trimmed reads to stdout (equivalent to justmp)
.TP
\fB\-\-stdout\-mp\fR
print only known MP reads to stdout (good for scaffolding)
.TP
\fB\-\-stdout\-un\fR
print only unknown reads to stdout
.TP
\fB\-\-rf\fR
leave mate pair reads in RF orientation [by default are flipped into FR]
.TP
\fB\-\-preserve\-mp\fR
preserve MPs even when the corresponding PE has longer reads
.TP
\fB\-\-ignorePF\fR
ignore chastity/purity filters in read headers
.TP
\fB\-\-separate\fR
output paired reads in separate files (prefix_R1/prefix_r2). Default is interleaved.
.TP
\fB\-a\fR, \fB\-\-aggressive\fR
more aggressive adapter search (see docs/adapter.md)
.TP
\fB\-s\fR, \fB\-\-similarity\fR arg (=0.85)
The minimum similarity between strings to be considered a match (Hamming distance divided by string length)
.TP
\fB\-v\fR, \fB\-\-minoverlap\fR arg (=12)
The minimum overlap to be considered for matching
.TP
\fB\-l\fR, \fB\-\-minlength\fR arg
(=21)      The minimum read length to output (smaller reads will be filtered)
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.