Bacterial Genomes Python Packages

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

magphi

A bioinformatics tool allowing for examnination and extraction of genomic features using seed sequences.

crispio

🌱 Designing CRISPRi experiments in bacteria

integron-finder

Integron Finder aims at detecting integrons in DNA sequences.

cogor

Package for improving the functional annotation of bacterial genomes, classification of protein-coding sequences into clusters of orthologous groups, and visualization of the final annotated genome.

stringmlst

Fast k-mer based tool for multi locus sequence typing (MLST)

strainscan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

nomenclator

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

taranys

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.