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Install

Install this package:

emerge -a sci-biology/bambus

If the package is masked, you can unmask it using the autounmask tool or standard emerge options:

autounmask sci-biology/bambus

Or alternatively:

emerge --autounmask-write -a sci-biology/bambus

Package Information

Description:

Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Homepage:

https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS https://sourceforge.net/projects/amos/files/bambus

License:

Artistic

Versions

Metadata

Description

• Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Maintainers

• Martin Mokrejs (mmokrejs@fold.natur.cuni.cz) - Type: person
• Gentoo Biology Project (sci-biology@gentoo.org) - Type: project

Upstream

• Remote IDs:
  • sourceforge: mira-assembler

<pkgmetadata>
	<maintainer type="person">
		<email>mmokrejs@fold.natur.cuni.cz</email>
		<name>Martin Mokrejs</name>
	</maintainer>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<longdescription>Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.</longdescription>
	<upstream>
		<remote-id type="sourceforge">mira-assembler</remote-id>
	</upstream>
</pkgmetadata>

Lint Warnings

• [Error] Missing md5-cache for ebuild bambus-2.33-r2

Files

• TigrFoundation-all-patches.patch
• goBambus.pl

Manifest