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@bacpop Bacterial population genetics

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    46 repositories

    • beebop

      Public
      Frontend code for beebop
      TypeScript
      •
      Other
      •0•1•4•4•Updated Jan 7, 2026Jan 7, 2026

    • ska.rust

      Public
      Split k-mer analysis – version 2
      rustbioinformaticsalignmentsequencek-merska
      Rust
      •
      Apache License 2.0
      •8•103•11•1•Updated Jan 7, 2026Jan 7, 2026

    • beebop_py

      Public
      Python API for beebop
      Python
      •0•0•0•4•Updated Jan 7, 2026Jan 7, 2026

    • PopPUNK

      Public
      PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
      genomicssketchingbacteriak-merpopulation-genetics
      Python
      •
      Apache License 2.0
      •19•102•37•0•Updated Jan 6, 2026Jan 6, 2026

    • PopPIPE

      Public
      Population analysis PIPEline 🛠🧬
      Python
      •
      Apache License 2.0
      •7•22•3•0•Updated Jan 5, 2026Jan 5, 2026

    • bacpop-website

      Public
      Code for group website
      bioinformaticsmodellingbacteriapopulation-genetics
      HTML
      •
      Apache License 2.0
      •8•1•0•0•Updated Jan 2, 2026Jan 2, 2026

    • Stubentiger

      Public
      An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
      C++
      •
      Apache License 2.0
      •1•3•0•0•Updated Dec 19, 2025Dec 19, 2025

    • sketchlib.rust

      Public
      Fast sequence distance estimates
      bioinformaticsgenomicssketchingk-mer
      Rust
      •
      Apache License 2.0
      •6•26•14•0•Updated Dec 18, 2025Dec 18, 2025

    • sparrowhawk-web

      Public
      Web interface for the sparrowhawk genome assembler using WebAssembly and Rust 🦅
      Vue
      •
      Apache License 2.0
      •1•1•8•1•Updated Dec 17, 2025Dec 17, 2025

    • TOMBOMBADIL_jax

      Public
      JAX prototype of TOMBOMBADIL
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • NFDS_Model

      Public
      Negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • unitig-caller

      Public
      Methods to determine sequence element (unitig) presence/absence
      C++
      •
      Apache License 2.0
      •3•22•13•0•Updated Nov 24, 2025Nov 24, 2025

    • biomics_website

      Public
      Website for BIOMICS hackathon
      SCSS
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • sparrowhawk

      Public
      Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅
      rustbioinformaticswebassemblygenome-assembly
      Rust
      •
      Apache License 2.0
      •2•11•10•0•Updated Nov 4, 2025Nov 4, 2025

    • Pansim

      Public
      Pangenome simulator
      Rust
      •
      MIT License
      •0•5•0•0•Updated Oct 27, 2025Oct 27, 2025

    • ggCaller

      Public
      Bifrost graph gene caller.
      C++
      •
      MIT License
      •6•97•3•0•Updated Sep 24, 2025Sep 24, 2025

    • beebop-deploy

      Public
      Deploy scripts for beebop
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • TOMBOMBADIL

      Public
      Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
      Stan
      •
      Apache License 2.0
      •0•5•0•0•Updated Jul 17, 2025Jul 17, 2025

    • SBMLtoOdin

      Public
      An R package for translating SBML models into odin models.
      R
      •
      Apache License 2.0
      •0•3•0•0•Updated Jun 20, 2025Jun 20, 2025

    • Menelmacar

      Public
      A viewer of odin.js models from the biomodels database
      JavaScript
      •
      MIT License
      •1•3•6•0•Updated Jun 20, 2025Jun 20, 2025

    • ska_simulations

      Public
      Mutation simulation to test ska.rust sensitivity
      Rust
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 12, 2025Jun 12, 2025

    • pp-sketchlib

      Public
      Library of sketching functions used by PopPUNK
      C++
      •
      Apache License 2.0
      •8•31•11•0•Updated Mar 31, 2025Mar 31, 2025

    • mandrake

      Public
      Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
      genomicsgpucudaembeddingpathogens
      Python
      •
      Apache License 2.0
      •2•39•4•0•Updated Mar 7, 2025Mar 7, 2025

    • compartmental-models-odin-dust

      Public
      A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.
      HTML
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 18, 2025Feb 18, 2025

    • trees_rs

      Public
      Tree inference in rust
      Rust
      •
      GNU Affero General Public License v3.0
      •1•2•6•0•Updated Jan 6, 2025Jan 6, 2025

    • beebop-k8s

      Public
      Shell
      •0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • readfish

      Public
      Read Until scripts with graph alignment
      Python
      •
      GNU General Public License v3.0
      •35•2•0•0•Updated Aug 22, 2024Aug 22, 2024

    • DATACIN

      Public
      Draw A Tree And Colour it IN
      Rust
      •1•1•4•0•Updated Aug 5, 2024Aug 5, 2024

    • CELEBRIMBOR

      Public
      Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
      metagenomicsbioinfomaticspangenomes
      Python
      •
      Apache License 2.0
      •1•25•3•0•Updated Jul 22, 2024Jul 22, 2024

    • adaptive_sampling_scripts

      Public
      Scripts for adaptive sampling analysis
      R
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Jul 3, 2024Jul 3, 2024