.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH MASAI_MAPPER "1" "September 2014" "masai_mapper 1.4.1+dfsg" "User Commands"
.SH NAME
masai_mapper \- Masai Mapper
.PP
SYNOPSIS
.IP
masai_mapper [OPTIONS] <GENOME FILE> <READS FILE>
.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
Mapping Options:
.HP
\fB\-mm\fR, \fB\-\-mapping\-mode\fR STR
.IP
Select mapping mode. One of all, all\-best, and any\-best. Default:
any\-best.
.HP
\fB\-mb\fR, \fB\-\-mapping\-block\fR NUM
.IP
Maximum number of reads to be mapped at once. In range [10000..inf].
Default: 2147483647.
.HP
\fB\-e\fR, \fB\-\-errors\fR NUM
.IP
Maximum number of errors per read. In range [0..32]. Default: 5.
.HP
\fB\-sl\fR, \fB\-\-seed\-length\fR NUM
.IP
Minimum seed length. In range [10..100]. Default: 33.
.HP
\fB\-ng\fR, \fB\-\-no\-gaps\fR
.IP
Do not align reads with gaps.
.IP
Genome Index Options:
.HP
\fB\-x\fR, \fB\-\-index\fR STR
.IP
Select the genome index type. One of esa, sa, qgram, and fm.
Default: sa.
.HP
\fB\-xp\fR, \fB\-\-index\-prefix\fR STR
.IP
Specify an genome index prefix name. Default: use the genome
filename prefix.
.IP
Output Options:
.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\-nv\fR, \fB\-\-no\-verify\fR
.IP
Do not verify seed hits.
.HP
\fB\-nd\fR, \fB\-\-no\-dump\fR
.IP
Do not dump results.
.HP
\fB\-nm\fR, \fB\-\-no\-multiple\fR
.IP
Disable multiple backtracking.
.PP
VERSION
.IP
masai_mapper version: 0.7.1 [14053]
Last update 2013\-05\-16