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masai_mapper - Online in the Cloud

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This is the command masai_mapper 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_mapper - Masai Mapper

SYNOPSIS

masai_mapper [OPTIONS] <GENOME FILE> <READS FILE>

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

Mapping Options:

-mm, --mapping-mode STR

Select mapping mode. One of all, all-best, and any-best. Default: any-best.

-mb, --mapping-block NUM

Maximum number of reads to be mapped at once. In range [10000..inf]. Default:
2147483647.

-e, --errors NUM

Maximum number of errors per read. In range [0..32]. Default: 5.

-sl, --seed-length NUM

Minimum seed length. In range [10..100]. Default: 33.

-ng, --no-gaps

Do not align reads with gaps.

Genome Index Options:

-x, --index STR

Select the genome index type. One of esa, sa, qgram, and fm. Default: sa.

-xp, --index-prefix STR

Specify an genome index prefix name. Default: use the genome filename prefix.

Output Options:

-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:

-nv, --no-verify

Do not verify seed hits.

-nd, --no-dump

Do not dump results.

-nm, --no-multiple

Disable multiple backtracking.

VERSION

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

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