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