/Mtb_genomic_lists

Curated lists of features for Mtb genomic analysis

Primary LanguageJupyter Notebook

Lists from multiple sources for use in Mtb genomics

Includes lists of genes to mask from variant coverage due to poor short read coverage (eg PE/PPE), genes associated with drug resistance, and gene annotations

Most folders contain

1) the original data, usually a supplementary file to a publication,

2) A Jupyter notebook to translate the original data into a more readable (for humans or computers) format, and

3) The output of that transformation

To make the Jupyter notebooks git friendly, follow the steps

  1. Install nbstripout pip install --upgrade nbstripout
  2. Set up the git filter using .gitattributes nbstripout --install --attributes .gitattributes