.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH MASAI_INDEXER "1" "September 2014" "masai_indexer 1.4.1+dfsg" "User Commands"
.SH NAME
masai_indexer \- Masai Indexer
.PP
SYNOPSIS
.IP
masai_indexer [OPTIONS] <GENOME 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
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\-t\fR, \fB\-\-tmp\-folder\fR STR
.IP
Specify a huge temporary folder. Default: use the genome folder.
.PP
VERSION
.IP
masai_indexer version: 0.7.1 [14053]
Last update 2013\-05\-16