pyfaidx

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

Deep learning-based variant caller

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

Scalable genomic analysis.

Python wrapper for [samtools](https://github.com/samtools/samtools).

k-mer counting, filtering, and graph traversal.