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MASAI_OUTPUT_PE(1) User Commands MASAI_OUTPUT_PE(1)

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
September 2014 masai_output_pe 1.4.1+dfsg