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**Documentation:** [https://cbg-ethz.github.io/covvfit](https://cbg-ethz.github.io/covvfit)\n  - **Source code:** [https://github.com/cbg-ethz/covvfit](https://github.com/cbg-ethz/covvfit)\n  - **Bug reports:** [https://github.com/cbg-ethz/covvfit/issues](https://github.com/cbg-ethz/covvfit/issues)\n\n\n## Installation and usage\n\n*Covvfit* can be installed from the Python Package Index:\n\n```bash\n$ pip install covvfit\n```\n\nFor an example how to analyze the data see [this tutorial](https://cbg-ethz.github.io/covvfit/cli/).\n\n\n## References\n\nThis method accompanies our manuscript:\n\nDavid Dreifuss, Paweł Piotr Czyż, Niko Beerenwinkel. *Learning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit*. medRxiv 2025.03.25.25324639; doi: [https://doi.org/10.1101/2025.03.25.25324639](https://doi.org/10.1101/2025.03.25.25324639)\n\n\n```bibtex\n@article{Dreifuss2025-Covvfit,\n\tauthor = {Dreifuss, David and Czy{\\.z}, Pawe{\\l} Piotr and Beerenwinkel, Niko},\n\ttitle = {Learning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit},\n\telocation-id = {2025.03.25.25324639},\n\tyear = {2025},\n\tdoi = {10.1101/2025.03.25.25324639},\n\tpublisher = {Cold Spring Harbor Laboratory Press},\n\teprint = {https://www.medrxiv.org/content/early/2025/03/26/2025.03.25.25324639.full.pdf},\n\tjournal = {medRxiv}\n}\n```\n\n\n## See Also\n\n  - [V-pipe](https://cbg-ethz.github.io/V-pipe/): a bioinformatics pipeline for viral sequencing data.\n  - [cojac](https://github.com/cbg-ethz/cojac): command-line tools for the analysis of co-occurrence of mutations on amplicons.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fcovvfit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fcovvfit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fcovvfit/lists"}