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

treesapp

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

cogclassifier

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

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

aniclustermap

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

genegrouper

Find and cluster genomic regions containing a seed gene

gbkviz

Simple web application to visualize and compare genomes in Genbank files

lissero

In silico serotyping of Listeria monocytogenes

albatradis

Comparitive transposon mutagenesis experiment analysis

biodive

Discovery of k-mer sequences associated with high rates of sequence diversification.

seroepi

A Python library for bacterial sero-epidemiology

mdu-pytools

Small tools/scripts written in Python for MDU

mgcplotter

Microbial Genome Circular plotting tool using Circos

metasbt

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

qiime-tools

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

phylotoast

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