Bacteria Python Packages

ppanggolin

Build a partitioned pangenome graph from microbial genomes

pioreactor

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

chewbbaca

BSR-Based Allele Calling Algorithm

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

pykinbiont

Python interface for KinBiont.jl microbial kinetics analysis

prfect

Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes

scoary

Pan-genome wide association studies

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

bacant

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria

amira-amr

A tool to detect acquired AMR genes directly from long read sequencing data.

cb-platon

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

acidoseq

Studying Acidobacteria reads

chewbbaca-nserver

BSR-Based Allele Calling Algorithm

crispio

🌱 Designing CRISPRi experiments in bacteria

pypangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

tadrep

Targeted Detection and Reconstruction of Plasmids

sismis

Machine learning-based secretion system annotation tool

decouphage

The art of decorating a phage genome by gluing feature cutouts into it.

pathogentrack

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.