Fitness estimates of SARS-CoV-2 variants.

Note: this package is in currently in an alpha stage. The API is expected to be refined and the documentation is being currently developed.

• Documentation: https://cbg-ethz.github.io/covvfit
• Source code: https://github.com/cbg-ethz/covvfit
• Bug reports: https://github.com/cbg-ethz/covvfit/issues

Create a new environment, e.g., using Micromamba:

$ micromamba create -n covvfit -c conda-forge python=3.11

Then, install the package.

For a machine where development happens it comes with developer utilities:

$ pip install poetry
$ poetry install --with dev
$ pre-commit install

• V-pipe: a bioinformatics pipeline for viral sequencing data.
• cojac: command-line tools for the analysis of co-occurrence of mutations on amplicons.