fermi-lite

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

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

A haplotype-resolved assembler for accurate Hifi reads.