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Install

Install this package:

emerge -a sci-biology/bismark

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

autounmask sci-biology/bismark

Or alternatively:

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

Package Information

Description:

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: (1) Bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignments; (3) Supports ungapped and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context.

Homepage:

https://www.bioinformatics.babraham.ac.uk/projects/

License:

GPL-3+

Versions

Metadata

Description

• Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: (1) Bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignments; (3) Supports ungapped and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context.

Maintainers

• Linlin Yan (yanlinlin82@gmail.com) - Type: person
• Gentoo Biology Project (sci-biology@gentoo.org) - Type: project

Upstream

• Remote IDs:
  • github: FelixKrueger/Bismark

<pkgmetadata>
	<maintainer type="person">
		<email>yanlinlin82@gmail.com</email>
		<name>Linlin Yan</name>
	</maintainer>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<longdescription lang="en">
Bismark is a program to map bisulfite treated sequencing reads to a genome of
interest and perform methylation calls in a single step. The output can be
easily imported into a genome viewer, such as SeqMonk, and enables a researcher
to analyse the methylation levels of their samples straight away. It's main
features are: (1) Bisulfite mapping and methylation calling in one single step;
(2) Supports single-end and paired-end read alignments; (3) Supports ungapped
and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
and CHH context.
</longdescription>
	<upstream>
		<remote-id type="github">FelixKrueger/Bismark</remote-id>
	</upstream>
</pkgmetadata>

Lint Warnings

• [Error] Missing md5-cache for ebuild bismark-0.23.0

Manifest