Microbial Genomics Python Packages

pygenomeviz

A genome visualization python package for comparative genomics

pycirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

ppanggolin

Build a partitioned pangenome graph from microbial genomes

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

kaptive

The tool for in silico serotyping

treesapp

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

genome-comparator

Fast genome comparison with Mash, from assemblies or reads: distance matrix, UPGMA/NJ/ME trees with bootstrap support, and interactive PCoA

genegrouper

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

panorama-sys

PANORAMA Project

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

gbkviz

Easy-to-use web application for visualization and comparison of genomes in Genbank file

lissero

In silico serotype prediction for Listeria monocytogenes

mgcplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

leviathan

Leviathan: Fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics

metasbt

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

albatradis

Comparative TraDIS analysis

qiime-tools

Tools for phylogenetic data analysis including visualization and cluster-computing support.

mdu-pytools

Small tools/scripts written in python

biodive

A reference-free statistical approach to diversity-generating & mobile genetic element discovery

phylotoast

Tools for phylogenetic data analysis including visualization and cluster-computing support.

seroepi

🦠💉🌍 A Python library for bacterial sero-epidemiology