QuaC
QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data - Published in JOSS (2023)
Science Score: 98.0%
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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 9 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
2 of 5 committers (40.0%) from academic institutions -
✓Institutional organization owner
Organization uab-cgds-worthey has institutional domain (sites.uab.edu) -
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Repository
🦆 Quality Control of WGS and exome samples 🦆
Basic Info
- Host: GitHub
- Owner: uab-cgds-worthey
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://quac.readthedocs.io
- Size: 37.5 MB
Statistics
- Stars: 6
- Watchers: 3
- Forks: 1
- Open Issues: 15
- Releases: 10
Topics
Metadata Files
README.md
QuaC
🦆🦆 Don't duck that QC thingy 🦆🦆
NOTE: In a past life, QuaC used a different remote Git management provider, UAB Gitlab. It was migrated to Github in Jan 2023, and the Gitlab version has been archived.
What is QuaC?
QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results using pre-defined, configurable QC thresholds.
In summary, QuaC performs the following:
- Runs several QC tools using
BAMandVCFfiles as input. At our center CGDS, these files are produced as part of the small variant caller pipeline. - Using QuaC-Watch tool, it performs QC checkup based on the expected thresholds for certain QC metrics and summarizes the results for easier human consumption
- Aggregates QC output as well as QuaC-Watch output using MulitQC, both at the sample level and project level.
- Optionally, above mentioned QuaC-Watch and QC aggregation steps can accept pre-run results from few QC tools (fastqc,
fastq-screen, picard's markduplicates) when run with flag
--include_prior_qc.
NOTE: QuaC is built to use with Human WGS/WES data. If you would like to use it with non-human data, please modify the pipeline as needed -- especially the thresholds used in QuaC-Watch configs.
Documentation
Full documentation, including installation and how to run QuaC, is available at https://quac.readthedocs.io.
Citing QuaC
If you use QuaC, please cite:
Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, https://doi.org/10.21105/joss.05313
Repo owner
- Manavalan Gajapathy
License
Contributing
See here for contributing guidelines.
Changelog
See here
Owner
- Name: Center for Computational Genomics and Data Science (CGDS)
- Login: uab-cgds-worthey
- Kind: organization
- Website: https://sites.uab.edu/cgds/
- Repositories: 2
- Profile: https://github.com/uab-cgds-worthey
JOSS Publication
QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data
Authors
Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Editor
Lorena Pantano
Tags
snakemake quality control genome sequencing exome sequencing QC review multiqc singularity bam vcfGitHub Events
Total
- Release event: 1
- Delete event: 1
- Issue comment event: 2
- Push event: 20
- Pull request review event: 4
- Pull request event: 4
- Create event: 3
Last Year
- Release event: 1
- Delete event: 1
- Issue comment event: 2
- Push event: 20
- Pull request review event: 4
- Pull request event: 4
- Create event: 3
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Manavalan Gajapathy | m****g@u****u | 500 |
| Manavalan Gajapathy | m****g@g****m | 110 |
| Brandon M. Wilk | w****7@g****m | 2 |
| dependabot[bot] | 4****] | 1 |
| Manavalan Gajapathy - UAB | u****1@d****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 73
- Total pull requests: 26
- Average time to close issues: about 1 year
- Average time to close pull requests: 5 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 2.3
- Average comments per pull request: 0.65
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 16 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ManavalanG (68)
- Redmar-van-den-Berg (2)
- wilkb777 (1)
- brentp (1)
Pull Request Authors
- ManavalanG (23)
- wilkb777 (2)
- dependabot[bot] (1)