Projects in Awesome Lists tagged with bacteria

https://github.com/tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

bacteria bioinformatics fastq-analysis genomics haploid indel-discovery snps variant-calling vcf

Last synced: 12 Apr 2025

https://github.com/oschwengers/bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

annotation bacteria bacterial-genomes bioinformatics genome-annotation mag metagenome-assembled-genomes microbial-genomics plasmids

Last synced: 14 May 2025

https://github.com/AdmiralenOla/Scoary

Pan-genome wide association studies

bacteria gene-presence-absence genomics gwas pan-genome

Last synced: 02 Apr 2025

https://github.com/pioreactor/pioreactor

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

algae bacteria biology bioreactor biotech educators evolution fermentation hardware mqtt raspberry-pi raspberrypi science yeast

Last synced: 23 Feb 2026

https://github.com/tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

bacteria denovo-assembly fastq genotyping phylogenomics public-health report resistome variant-calling virulome

Last synced: 12 Apr 2025

https://github.com/eead-csic-compbio/get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

annotation bacteria clustering fasta genbank pangene pangenome plants transcriptome

Last synced: 11 Feb 2026

https://github.com/oschwengers/platon

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

assembly bacteria bioinformatics contigs microbiology ngs plasmids wgs

Last synced: 12 Aug 2025

https://github.com/neherlab/pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

bacteria bioinformatics genome genome-assembly julia pangenome pangraph

Last synced: 04 Apr 2025

https://github.com/oschwengers/asap

A scalable bacterial genome assembly, annotation and analysis pipeline

amr annotation assembly bacteria bioinformatics ngs

Last synced: 16 Apr 2025

https://github.com/kjolley/BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

bacteria bioinformatics database genomes mlst typing

Last synced: 30 Mar 2025

https://github.com/johnlees/seer

sequence element (kmer) enrichment analysis

bacteria gwas k-mer

Last synced: 14 Aug 2025

https://github.com/tseemann/phastaf

Identify phage regions in bacterial genomes for masking purposes

bacteria bioinformatics genomics phage

Last synced: 15 Feb 2026

https://github.com/tseemann/sixess

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

bacteria fastq genomics species

Last synced: 12 Apr 2025

https://github.com/karel-brinda/phylign

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny

Last synced: 04 Mar 2025

https://github.com/karel-brinda/miniphy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny prophyle

Last synced: 10 Mar 2026

https://github.com/oschwengers/tadrep

Targeted Detection and Reconstruction of Plasmids

bacteria plasmids wgs

Last synced: 04 Mar 2026

https://github.com/mbhall88/nanovarbench

Evaluating Nanopore-based bacterial variant calling

bacteria benchmark bioinformatics illumina microbial-genomics nanopore variant-calling

Last synced: 03 Mar 2026

https://github.com/xthua/bacant

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

amr bacteria fasta integron transposon

Last synced: 14 Jan 2026

https://github.com/lmc297/bactaxr

Bacterial taxonomy construction and evaluation in R

ani average-nucleotide-identity bacteria bacterial-species medoid-genomes phylogeny taxonomy

Last synced: 22 Jan 2026

https://github.com/m-jahn/genome-scale-models

Genome scale metabolic models in SBML format

bacteria computational-biology genome-scale-models microbiology python3 sbml-models

Last synced: 23 Aug 2025

https://github.com/danderson123/amira

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

amr assembly bacteria bacterial-genome-analysis epidemiology genotyping graph

Last synced: 15 Apr 2025

https://github.com/deprekate/prfect

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

annotation bacteria bioinformatics genes genomics phages

Last synced: 23 Mar 2025

https://github.com/johannahelene/gemsparcl

gemsparcl 💎✨ Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life

bacteria genomics k-mers sketching

Last synced: 28 May 2026

https://github.com/zabuzard/antigen

Strategy game with cells, bacteria and viruses as units.

antigen bacteria game-design game-design-document gdd real-time-strategy scrum scrum-agile software-development strategy-game team-repo top-down viruses visual-studio

Last synced: 19 Sep 2025

https://github.com/karel-brinda/phylogenetic-compression-supplement

Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny

Last synced: 09 Feb 2026

https://github.com/nvladimus/rapidcell

Multiscale modeling of E.coli chemotaxis

bacteria chemotaxis modeling

Last synced: 13 May 2026

https://github.com/notthestallion/computer-vision-in-the-service-of-bacteriology

Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

bacteria bacterial bacterial-database bacterial-genome-analysis bacterial-genomes bash computer-vision learning opencv

Last synced: 02 May 2026

https://github.com/pseudogene/contiguator

A bacterial genomes finishing tool for structural insights on draft genomes - Now in a Docker

bacteria bioinformatics docker genome

Last synced: 12 Aug 2025

https://github.com/engineerdanny/cs685-microbe-network-research-code

This repo contains my cross-validation ML analysis for training and testing co-occurrence network inference algorithms

bacteria cross-validation ml network-analysis python

Last synced: 18 Apr 2026

https://github.com/schlosslab/hannigan_conjunctisviribus_ploscompbio_2018

Using graph database techniques to understand the infectious relationships between bacteria and phages.

bacteria microbiome phage phage-bacteria-networks reproducible-paper

Last synced: 23 Feb 2026

https://github.com/emanuelhuber/gwmodbac

Groundwater flow and microbes transport modelling with R and Modflow / Modpath

bacteria groundwater modeling modflow-usg modpath

Last synced: 14 Jul 2025

https://github.com/phac-nml/venae

A workflow to rapidly identify species and antimicrobial resistance genes in positive blood cultures sequenced using Oxford Nanopore Technologies (ONT)

antimicrobial-resistance assembly bacteria bioinformatics fungi metagenomics nextflow pipelines public-health quality-control report

Last synced: 16 Jan 2026

https://github.com/yanndubs/modellingbacterias

Useless project that tries to model the life of different bacterias in a petri dish: for learning purpose

bacteria bioinformatics modeling simulation

Last synced: 18 Mar 2025

https://github.com/davidegat/gameofbacteria

An educational simple game in Italian/English that simulates interaction between antbiotics and bacteria.

ai-assisted-development ai-coded ai-generated ai-music antibiotic-resistance antibiotics bacteria educational-game game learning medical pygame python simulation simulator teachers teaching-materials videogame

Last synced: 27 Feb 2025

https://github.com/kronopt/simulate

Simulator of Antibiotic Therapy Effects on the Dynamics of Bacterial Populations

antibiotic-resistance bacteria enterotype kivy microbiome python python-2 simulation

Last synced: 03 Oct 2025

https://github.com/emptyport/bacterial_proteomes

Scripts to investigate relationships between proteins between species of bacteria

bacteria bioinformatics python

Last synced: 29 Mar 2025

https://github.com/k8hertweck/bacterialgenomics

example genomics workflow for student training

bacteria genome-assembly genomics variant-calling

Last synced: 10 May 2026

https://github.com/k8hertweck/clostridium

assembly bacteria

Last synced: 11 May 2026

https://github.com/bneumann/alveolus-game

Unity "game" template with a simulation of bacterial pneumococcal pneumonia infection.

bacteria game gameification hackathon unity

Last synced: 11 Apr 2026

https://github.com/srom/archaea-vs-bacteria

Code from paper "Archaea produce peptidoglycan hydrolases that kill bacteria"

antimicrobial archaea bacteria microbiology phylogenetics

Last synced: 22 Jan 2026

https://github.com/sap218/acidoseq

A Python package for studying Acidobacteria

bacteria bioinformatics nanopore plotting python python3

Last synced: 22 Jan 2026

https://github.com/leylabmpi/traitar3

archaea bacteria genomes machine-learning phenotypes

Last synced: 18 Apr 2026

https://github.com/davidegat/antibiogramsimulator

A simple simulator that shows the easy way how an antibiogram works

ai-assisted-development ai-coded ai-generated ai-music antibiotic-resistance antibiotics bacteria educational-game game learning medical pygame python simulation simulator teachers teaching-materials videogame

Last synced: 12 Jun 2026

https://github.com/afm719/antibacterialai

The goal of this project is to apply Deep Learning techniques to generate novel candidate molecules with potential antibacterial activity. We aim to develop a generative model that learns from known antibacterial molecules and creates new molecular structures that could act as antibiotics.

antibiotics artificial-intelligence bacteria deep-learning molecule pharmacy variational-autoencoder