https://github.com/cbg-ethz/pangolin
BSSE COVID-19 sequencing of test swab samples
Science Score: 57.0%
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
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 5 committers (80.0%) from academic institutions -
✓Institutional organization owner
Organization cbg-ethz has institutional domain (www.bsse.ethz.ch) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.0%) to scientific vocabulary
Repository
BSSE COVID-19 sequencing of test swab samples
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- Language: Shell
- Default Branch: master
- Size: 2.85 MB
Statistics
- Stars: 7
- Watchers: 5
- Forks: 3
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
pangolin
This is a SARS-CoV-2 sequencing project done at the BSSE relying on V-pipe (doi:10.1093/bioinformatics/btab015) to analyse Illumina data done on positive swabs test samples for the genomic surveillance of the COVID-19 pandemic in Switzerland and on wastewater samples provided by EPFL and Eawag.
pipeline
for the V-pipe pipeline, see:
- tutorial: https://cbg-ethz.github.io/V-pipe/tutorial/sars-cov2/ (video tutorial)
- SARS-CoV-2 subpage: https://cbg-ethz.github.io/V-pipe/sars-cov-2/
- main website: https://cbg-ethz.github.io/V-pipe/
- github repo: https://github.com/cbg-ethz/V-pipe
wastewater
for the code used in wastewater analysis, see:
- https://github.com/cbg-ethz/cojac
video presentation
Short Oral presentation done at the ECCVID conference in September 2020:
- https://youtu.be/BJ-un88CT9A
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
- Issues event: 2
- Delete event: 5
- Issue comment event: 7
- Member event: 1
- Push event: 153
- Pull request review comment event: 6
- Pull request review event: 9
- Pull request event: 29
- Create event: 13
Last Year
- Issues event: 2
- Delete event: 5
- Issue comment event: 7
- Member event: 1
- Push event: 153
- Pull request review comment event: 6
- Pull request review event: 9
- Pull request event: 29
- Create event: 13
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ivan Blagoev Topolsky | i****y@b****h | 246 |
| Matteo Carrara | c****a@n****h | 18 |
| Uwe Schmitt | u****t@i****h | 9 |
| pedrofale | p****a@b****h | 2 |
| dr-david | d****s@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 2
- Total pull requests: 35
- Average time to close issues: about 2 months
- Average time to close pull requests: 2 months
- Total issue authors: 2
- Total pull request authors: 6
- Average comments per issue: 3.0
- Average comments per pull request: 0.57
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 16
- Average time to close issues: about 2 months
- Average time to close pull requests: 1 day
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 6.0
- Average comments per pull request: 0.06
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kirschen-k (1)
- mcarrara-bioinfo (1)
Pull Request Authors
- mcarrara-bioinfo (17)
- kirschen-k (10)
- uweschmitt (4)
- pedrofale (1)
- DrYak (1)
- dr-david (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- psycopg2 *
- sqlalchemy *