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       masai_mapper - Masai Mapper


              masai_mapper [OPTIONS] <GENOME FILE> <READS FILE>


              Masai  is  a  fast and accurate read mapper based on approximate
              seeds and multiple backtracking.

              See for more information.

              (c) Copyright 2011-2012 by Enrico Siragusa.

       -h, --help

              Displays this help message.


              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.


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

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