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