NAME

       masai_output_pe - Masai Output - Paired End Mode

       SYNOPSIS

              masai_output_pe  [OPTIONS] <GENOME FILE> <READS FILE L> <READS FILE R> <RAW FILE L>
              <RAW FILE R>

       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

              Pairing Options:

       -ng, --no-gaps

              Do not align reads with gaps.

       -ll, --library-length NUM

              Library length. Default: 220.

       -le, --library-error NUM

              Library length tolerance. Default: 50.

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