https://github.com/cancerit/cgp-methpipe
CGP implementation of Nextflow methylseq
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (2.4%) to scientific vocabulary
Last synced: 9 months ago
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Repository
CGP implementation of Nextflow methylseq
Basic Info
- Host: GitHub
- Owner: cancerit
- Language: Shell
- Default Branch: develop
- Size: 20.5 KB
Statistics
- Stars: 0
- Watchers: 8
- Forks: 1
- Open Issues: 1
- Releases: 0
Created almost 7 years ago
· Last pushed over 1 year ago
Metadata Files
Changelog
https://github.com/cancerit/cgp-methpipe/blob/develop/
# cgp-methpipe
This repository contains the tools used in Sanger's Cancer, Ageing and Somatic
Mutation group's methylation pipeline, containerised using Docker.
## Usage
```
docker run --rm cgp-methpipe:${VERSION} ${COMMAND}
```
### Commands
- fastqc
- cutadapt
- trim_galore
- bismark
- deduplicate_bismark
- bismark_methylation_extractor
- bismark2report
- bismark2summary
- samtools
- hisat2
- bwa
- bwameth.py
- picard
- MethylDackel
- qualimap
- preseq
- multiqc
- runMethPipe.sh
Owner
- Name: CASM IT
- Login: cancerit
- Kind: organization
- Email: cgpit@sanger.ac.uk
- Location: Hinxton, Cambridge, UK
- Website: http://www.sanger.ac.uk/science/programmes/cancer-genetics-and-genomics
- Repositories: 89
- Profile: https://github.com/cancerit
CASM IT provide bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Sanger Institute
GitHub Events
Total
- Delete event: 3
- Push event: 5
- Pull request event: 2
- Create event: 2
Last Year
- Delete event: 3
- Push event: 5
- Pull request event: 2
- Create event: 2