---
name: "masai_output_se"
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_output_se"
---

# masai\_output\_se(1)

Masai Output - Single End Mode SYNOPSIS DESCRIPTION -h, --help --version -ng, --no-gaps -m, --matches NUM -t, --tmp-folder STR -o, --output-file FILE -nc, --no-cigar -nd, --no-dump VERSION

## NAME

masai\_output\_se - Masai Output - Single End Mode

SYNOPSIS

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  masai\_output\_se \[OPTIONS\] \<GENOME FILE\> \<READS FILE\> \<RAW FILE\>

DESCRIPTION

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  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.

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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:

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

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  Do not align reads with gaps.

**-m**, **--matches** NUM

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  Maximum number of matches per read.

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  Output Options:

**-t**, **--tmp-folder** STR

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  Specify a huge temporary folder. Default: use the genome folder.

**-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:

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

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  Do not dump results.

VERSION

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