Microbiology Python Packages

splicecraft

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

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

ppanggolin

Build a partitioned pangenome graph from microbial genomes

drep

Rapid comparison and dereplication of genomes

pyani-plus

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

binette

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

mlstclassifier-cd

multi-locus sequence type clade classifier for Clostridioides difficile

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

mgkit

MGKit: Metagenomics Framework

cb-platon

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

referenceseeker

Rapid determination of appropriate reference genomes.

pykinbiont

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

tunacell

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

calcfu

CFU calculator based on NCIMS 2400s SOPs.

nomenclator

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

grna-create

A tool to create gRNAs

parmmosahn

PaRMMoSaHN - Pangenome Reference-based Metabolic Modelling by Saving Homolog Networks

plasmidcanvas

A graphics package for creating customised plasmid maps