Microbiology Python Packages

splicecraft

In-Terminal Plasmid Design Workbench

34K 74 5

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.

28K 110 23

ppanggolin

Build a partitioned pangenome graph from microbial genomes

9K 301 29

pygenomeviz

A genome visualization python package for comparative genomics

5K 403 25

binette

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

1K 50 2

mgkit

Metagenomics Framework

920 15 3

drep

Rapid comparison and dereplication of genomes

915 340 41

mlstclassifier-cd

multi-locus sequence type clade classifier for C.difficile

831 0 0

pyani-plus

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

771 33 2

cb-platon

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.

446 121 15

referenceseeker

ReferenceSeeker: rapid determination of appropriate reference genomes.

279 101 7

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

231 27 0

pykinbiont

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

212 0 0