Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository bismark
Name: bismark
Owner: bgruening
Synopsis: A tool to map bisulfite converted sequence reads and determine cytosine methylation states
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:
- Bisulfite mapping and methylation calling in one single step
- Supports single-end and paired-end read alignments
- Supports ungapped and gapped alignments
- Alignment seed length, number of mismatches etc. are adjustable
- Output discriminates between cytosine methylation in CpG, CHG and CHH context
http://www.bioinformatics.babraham.ac.uk/projects/bismark/
Type: unrestricted
Revision: 21:120b7b35e442
This revision can be installed: True
Times cloned / installed: 3022

Contents of this repository

Name Description Version Minimum Galaxy Version
Reports on methylation status of reads mapped by Bismark 0.22.1 18.01
Generates a graphical HTML report page from report outputs of Bismark 0.22.1 17.01
Bisulfite reads mapper 0.22.1+galaxy4 18.01
Deduplicates reads mapped by Bismark 0.22.1 18.01

Categories
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data