hifiasm

Deep learning-based variant caller

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.

A fuzzy Bruijn graph approach to long noisy reads assembly

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF.

A polymorphic bayesian genotyping model with wide applicability.