Microbiology Python Packages

amr

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

pygenomeviz

A genome visualization python package for comparative genomics

splicecraft

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

ppanggolin

Build a partitioned pangenome graph from microbial genomes

gambit

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

drep

Rapid comparison and dereplication of genomes

minerva-dna

Coevolutionary discovery using genome language models

binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

pyani-plus

Development repo for pyani-plus (the next iteration of pyani)

mgkit

MGKit: Metagenomics Framework

panorama-sys

PANORAMA Project

cb-platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

phagemine

Phage-focused genome annotation and comparative genomics workflow integrating structural gene prediction, evidence-supported functional annotation, and INPHARED nearest-phage analysis.

referenceseeker

Rapid determination of appropriate reference genomes.

mlstclassifier-cd

multi-locus sequence type clade classifier for Clostridioides difficile

automator-tsl

Research automation system for imaging microbial plates [Magnaporthe Orzae]

calcfu

CFU calculator based on NCIMS 2400s SOPs.

plasmidcanvas

A simple python plasmid map creator

pykinbiont

Python interface for KinBiont.jl. Model-based analysis of microbial growth kinetics from Julia, accessible in Python with native numpy and pandas support.

grna-create

Tool to design gRNAs

nomenclator

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

tunacell

A library for analyzing time-series of dividing micro-organisms

parmmosahn

Species-agnostic pipeline that builds a pangenome-reference metabolic model and rapidly derives consistent, gap-filled strain-specific genome-scale models from bacterial genomes.