This is the command masai_mapper that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
masai_mapper - Masai Mapper
SYNOPSIS
masai_mapper [OPTIONS] <GENOME FILE> <READS FILE>
DESCRIPTION
Masai is a fast and accurate read mapper based on approximate seeds and multiple
backtracking.
See http://www.seqan.de/projects/masai for more information.
(c) Copyright 2011-2012 by Enrico Siragusa.
-h, --help
Displays this help message.
--version
Display version information
Mapping Options:
-mm, --mapping-mode STR
Select mapping mode. One of all, all-best, and any-best. Default: any-best.
-mb, --mapping-block NUM
Maximum number of reads to be mapped at once. In range [10000..inf]. Default:
2147483647.
-e, --errors NUM
Maximum number of errors per read. In range [0..32]. Default: 5.
-sl, --seed-length NUM
Minimum seed length. In range [10..100]. Default: 33.
-ng, --no-gaps
Do not align reads with gaps.
Genome Index Options:
-x, --index STR
Select the genome index type. One of esa, sa, qgram, and fm. Default: sa.
-xp, --index-prefix STR
Specify an genome index prefix name. Default: use the genome filename prefix.
Output Options:
-o, --output-file FILE
Specify an output file. Default: use the reads filename prefix. Valid filetypes
are: raw and sam.
-nc, --no-cigar
Do not output CIGAR string. This only affects SAM output.
Debug Options:
-nv, --no-verify
Do not verify seed hits.
-nd, --no-dump
Do not dump results.
-nm, --no-multiple
Disable multiple backtracking.
VERSION
masai_mapper version: 0.7.1 [14053] Last update 2013-05-16
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