Bacterial Genomes Python Packages

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

crispio

Designing CRISPR-Cas guide RNAs in bacteria.

magphi

Tool intended to pull out sequences and annotations between insertion sites specified by the user.

strainscan

One efficient and accurate strain-level microbiome composition analysis tool based on reference genomes and k-mers.

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)

integron-finder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

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.