https://github.com/cbg-ethz/haploclique
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 11 committers (9.1%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Keywords
Repository
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
Basic Info
Statistics
- Stars: 25
- Watchers: 12
- Forks: 32
- Open Issues: 12
- Releases: 0
Topics
Metadata Files
README.md
We present a novel method to reconstruct the structure of a viral quasispecies from NGS data. Our approach can be used to: - reconstruct local error-corrected haplotypes and estimate their abundance - assemble full-length viral haplotypes - detect large deletions and insertions from paired-end data.
Reference implementation of:
Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, and Niko Beerenwinkel. Viral quasispecies assembly via maximal clique finding PLOS Computational Biology, 2014.
Documentation
Contributions
- Armin Töpfer
- Tobias Marschall
- Maryam Zaheri
- Bernhard Lang
- Marcel Meyerheim
- The HaploClique implementation was derived from CLEVER
Contact
Please use the issue tracker
Build
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Armin Töpfer | a****r@g****m | 108 |
| Tesafilm1 | m****m@f****e | 71 |
| MaryamZaheri | z****m@b****h | 14 |
| Bernhard Lang | b****g@g****e | 7 |
| MaryamZaheri | z****i@g****m | 4 |
| Tobias Marschall | t****l@0****t | 2 |
| DrYak | d****k@g****m | 2 |
| Riccardo Murri | r****i@g****m | 1 |
| David Seifert | s****p@s****t | 1 |
| Tobias Marschall | T****l@c****l | 1 |
| David Seifert | g****t@s****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 36
- Total pull requests: 28
- Average time to close issues: 5 months
- Average time to close pull requests: 8 days
- Total issue authors: 16
- Total pull request authors: 5
- Average comments per issue: 1.97
- Average comments per pull request: 0.75
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- armintoepfer (14)
- jacobhurst (4)
- tobiasmarschall (2)
- daveuu (2)
- jblamyatifremer (2)
- seoanezonjic (2)
- shounak1990 (1)
- ghost (1)
- antoine4ucsd (1)
- natasacirovic (1)
- ruby-r (1)
- som1234 (1)
- Ruchank1 (1)
- DrYak (1)
- bgruening (1)
Pull Request Authors
- MaryamZaheri (18)
- armintoepfer (5)
- DrYak (3)
- riccardomurri (1)
- Tesafilm1 (1)