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masai_output_pe - Online in the Cloud

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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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