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@bacpop

Bacterial population genetics

Pathogen Informatics and Modelling @ EMBL-EBI / Bacterial Evolutionary Epidemiology Group @ Imperial College London

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  1. PopPUNK PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Python 105 21

  2. ggCaller ggCaller Public

    Bifrost graph gene caller.

    C++ 98 6

  3. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 104 8

  4. unitig-caller unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    C++ 23 3

  5. PopPIPE PopPIPE Public

    Population analysis PIPEline 🛠🧬

    Python 23 7

  6. sketchlib.rust sketchlib.rust Public

    Fast sequence distance estimates

    Rust 27 6

Repositories

Showing 10 of 47 repositories
  • sparrowhawk-web Public

    Web interface for the sparrowhawk genome assembler using WebAssembly and Rust 🦅

    bacpop/sparrowhawk-web’s past year of commit activity
    Vue 1 Apache-2.0 1 8 0 Updated Mar 20, 2026
  • bacpop-website Public

    Code for group website

    bacpop/bacpop-website’s past year of commit activity
    HTML 1 Apache-2.0 8 0 0 Updated Mar 20, 2026
  • Stubentiger Public

    An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations

    bacpop/Stubentiger’s past year of commit activity
    C++ 4 Apache-2.0 1 1 (1 issue needs help) 0 Updated Mar 19, 2026
  • NFDS_Model Public

    Negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations

    bacpop/NFDS_Model’s past year of commit activity
    R 0 Apache-2.0 0 0 0 Updated Mar 16, 2026
  • biomics_website Public

    Website for BIOMICS hackathon

    bacpop/biomics_website’s past year of commit activity
    SCSS 0 4 0 1 Updated Mar 14, 2026
  • TOMBOMBADIL_jax Public

    JAX prototype of TOMBOMBADIL

    bacpop/TOMBOMBADIL_jax’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Mar 13, 2026
  • sketchlib.rust Public

    Fast sequence distance estimates

    bacpop/sketchlib.rust’s past year of commit activity
    Rust 27 Apache-2.0 6 14 0 Updated Mar 10, 2026
  • Menelmacar Public

    A viewer of odin.js models from the biomodels database

    bacpop/Menelmacar’s past year of commit activity
    JavaScript 4 MIT 1 6 0 Updated Mar 7, 2026
  • unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    bacpop/unitig-caller’s past year of commit activity
    C++ 23 Apache-2.0 3 13 0 Updated Mar 6, 2026
  • sparrowhawk Public

    Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅

    bacpop/sparrowhawk’s past year of commit activity
    Rust 12 Apache-2.0 2 10 0 Updated Mar 4, 2026
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