Search 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.

ppanggolin

Build a partitioned pangenome graph from microbial genomes

pygenomeviz

A genome visualization python package for comparative genomics

binette

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

mgkit

Metagenomics Framework

drep

Rapid comparison and dereplication of genomes

pykinbiont

Python interface for KinBiont.jl microbial kinetics analysis

pyani-plus

pyANI-plus is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity and similar methods.

referenceseeker

ReferenceSeeker: rapid determination of appropriate reference genomes.

mlstclassifier-cd

multi-locus sequence type clade classifier for Clostridioides difficile

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

cb-platon

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

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

calcfu

CFU calculator based on NCIMS 2400s SOPs.

plasmidcanvas

A simple python plasmid map creator