---
name: "masai_mapper"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "1.4.1+dfsg-2"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/masai_mapper"
---

# masai\_mapper(1)

Masai Mapper SYNOPSIS DESCRIPTION -h, --help --version -mm, --mapping-mode STR -mb, --mapping-block NUM -e, --errors NUM -sl, --seed-length NUM -ng, --no-gaps -x, --index STR -xp, --index-prefix STR -o, --output-file FILE -nc, --no-cigar -nv, --no-verify -nd, --no-dump -nm, --no-multiple VERSION

## NAME

masai\_mapper - Masai Mapper

SYNOPSIS

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  masai\_mapper \[OPTIONS\] \<GENOME FILE\> \<READS FILE\>

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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  Mapping Options:

**-mm**, **--mapping-mode** STR

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

**-mb**, **--mapping-block** NUM

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

**-e**, **--errors** NUM

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

**-sl**, **--seed-length** NUM

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

**-ng**, **--no-gaps**

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  Do not align reads with gaps.

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  Genome Index Options:

**-x**, **--index** STR

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

**-xp**, **--index-prefix** STR

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

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  Output Options:

**-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:

**-nv**, **--no-verify**

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  Do not verify seed hits.

**-nd**, **--no-dump**

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  Do not dump results.

**-nm**, **--no-multiple**

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  Disable multiple backtracking.

VERSION

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  masai\_mapper version: 0.7.1 \[14053\] Last update 2013-05-16