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.

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Mapping Options:

Select mapping mode. One of all, all-best, and any-best. Default: any-best.

Maximum number of reads to be mapped at once. In range [10000..inf]. Default: 2147483647.

Maximum number of errors per read. In range [0..32]. Default: 5.

Minimum seed length. In range [10..100]. Default: 33.

Do not align reads with gaps.

Genome Index Options:

Select the genome index type. One of esa, sa, qgram, and fm. Default: sa.

Specify an genome index prefix name. Default: use the genome filename prefix.

Output Options:

Specify an output file. Default: use the reads filename prefix. Valid filetypes are: raw and sam.

Do not output CIGAR string. This only affects SAM output.

Debug Options:

Do not verify seed hits.

Do not dump results.

Disable multiple backtracking.

VERSION

masai_mapper version: 0.7.1 [14053] Last update 2013-05-16