Bacteria Python Packages

ppanggolin

Build a partitioned pangenome graph from microbial genomes

8K 312 34

pioreactor

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

3K 149 18

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

2K 683 87

chewbbaca

BSR-Based Allele Calling Algorithm

2K 154 33

gtdbtk

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

1K 623 100

scoary

Pan-genome wide association studies

975 226 35

omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation

973 165 46

prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

768 38 5

gtdb-gtranslate

Tool for identifying the genetic translation table used by prokaryotic organisms

612 4 0

panorama-sys

PANORAMA Project

364 11 0

cb-platon

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

362 130 16

prfect

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

327 9 2

bacant

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

288 21 7

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

277 112 23

amira-amr

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

251 28 2

crispio

🌱 Designing CRISPRi experiments in bacteria

246 1 3

chewbbaca-nserver

BSR-Based Allele Calling Algorithm

217 154 33

pypangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

168 129 6

tadrep

Targeted Detection and Reconstruction of Plasmids

102 22 1

omnipose-acdc

Omnipose: a high-precision solution for morphology-independent cell segmentation

87 165 46

pykinbiont

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

86 0 0

sismis

Machine learning-based secretion system annotation tool

81 3 0

decouphage

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

78 5 2

pathogentrack

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

69 32 8