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.

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

chewbbaca

BSR-Based Allele Calling Algorithm

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

crispio

Designing CRISPR-Cas guide RNAs in bacteria.

gtdb-gtranslate

Tool for identifying the genetic translation table used by prokaryotic organisms

scoary

Pan-genome wide association studies

bacant

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

acidoseq

A Python package for studying Acidobacteria

cb-platon

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

prfect

A tool to predict programmed ribosomal frameshifts

amira-amr

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

chewbbaca-nserver

BSR-Based Allele Calling Algorithm

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

pypangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

pykinbiont

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

tadrep

Targeted Detection and Reconstruction of Plasmids

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.

sismis

Machine learning-based secretion system annotation tool