.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH MASAI_OUTPUT_PE "1" "September 2014" "masai_output_pe 1.4.1+dfsg" "User Commands"
.SH NAME
masai_output_pe \- Masai Output \- Paired End Mode
.PP
SYNOPSIS
.IP
masai_output_pe [OPTIONS] <GENOME FILE> <READS FILE L> <READS FILE R> <RAW
FILE L> <RAW FILE R>
.PP
DESCRIPTION
.IP
Masai is a fast and accurate read mapper based on approximate seeds and
multiple backtracking.
.IP
See http://www.seqan.de/projects/masai for more information.
.IP
(c) Copyright 2011\-2012 by Enrico Siragusa.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Pairing Options:
.HP
\fB\-ng\fR, \fB\-\-no\-gaps\fR
.IP
Do not align reads with gaps.
.HP
\fB\-ll\fR, \fB\-\-library\-length\fR NUM
.IP
Library length. Default: 220.
.HP
\fB\-le\fR, \fB\-\-library\-error\fR NUM
.IP
Library length tolerance. Default: 50.
.IP
Output Options:
.HP
\fB\-t\fR, \fB\-\-tmp\-folder\fR STR
.IP
Specify a huge temporary folder. Default: use the genome folder.
.HP
\fB\-o\fR, \fB\-\-output\-file\fR FILE
.IP
Specify an output file. Default: use the reads filename prefix.
Valid filetypes are: raw and sam.
.HP
\fB\-nc\fR, \fB\-\-no\-cigar\fR
.IP
Do not output CIGAR string. This only affects SAM output.
.IP
Debug Options:
.HP
\fB\-nd\fR, \fB\-\-no\-dump\fR
.IP
Do not dump results.
.PP
VERSION
.IP
masai_output_pe version: 0.7.1 [14053]
Last update 2013\-05\-16