NAME

       masai_output_se - Masai Output - Single End Mode

       SYNOPSIS

              masai_output_se [OPTIONS] <GENOME FILE> <READS FILE> <RAW 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:

       -ng, --no-gaps

              Do not align reads with gaps.

       -m, --matches NUM

              Maximum number of matches per read.

              Output Options:

       -t, --tmp-folder STR

              Specify a huge temporary folder. Default: use the genome folder.

       -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:

       -nd, --no-dump

              Do not dump results.

       VERSION

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