https://github.com/cbg-ethz/sars-cov-2-wastewater-sample-processing-viloca
wastewater-sample-processing-VILOCA
https://github.com/cbg-ethz/sars-cov-2-wastewater-sample-processing-viloca
Science Score: 26.0%
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
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (3.9%) to scientific vocabulary
Repository
wastewater-sample-processing-VILOCA
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: apache-2.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 1.23 MB
Statistics
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Wastewater sample processing
This workflow processes wastewater samples for the detection of drug resistance mutations.
Input: - aligned samples (alignment with V-pipe) - positions of interest: positions where drug resistance mutations are expected - list of all samples to be processed
Output: - csv file of all mutations at positions of interest --> This file can be used in the visualisation notebook to create a heatmap
To run this workflow adapt file paths in config and sample names. Run the pipeline on Euler with run_workflow.sh.
Note, at the moment the workflow is SARS-CoV-2 specific, however, reference files and gene annotations can be easily swapped.
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
- Release event: 1
- Watch event: 1
- Create event: 1
Last Year
- Release event: 1
- Watch event: 1
- Create event: 1
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- 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
Pull Request Authors
- LaraFuhrmann (4)