NAME
masai_output_pe - Masai Output - Paired End Mode
SYNOPSIS
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masai_output_pe [OPTIONS] <GENOME FILE> <READS FILE L> <READS FILE R> <RAW FILE L> <RAW FILE R>
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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Pairing Options:
-ng, --no-gaps
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Do not align reads with gaps.
-ll, --library-length NUM
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Library length. Default: 220.
-le, --library-error NUM
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Library length tolerance. Default: 50.
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Output Options:
-t, --tmp-folder STR
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Specify a huge temporary folder. Default: use the genome folder.
-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:
-nd, --no-dump
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Do not dump results.
VERSION
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masai_output_pe version: 0.7.1 [14053] Last update 2013-05-16