This is the command masai_output_pe that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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