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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 102 20

  2. ggCaller ggCaller Public

    Bifrost graph gene caller.

    C++ 97 6

  3. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 103 8

  4. unitig-caller unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    C++ 22 3

  5. PopPIPE PopPIPE Public

    Population analysis PIPEline 🛠🧬

    Python 22 7

  6. sketchlib.rust sketchlib.rust Public

    Fast sequence distance estimates

    Rust 26 6

Repositories

Showing 10 of 46 repositories
  • biomics_website Public

    Website for BIOMICS hackathon

    bacpop/biomics_website’s past year of commit activity
    SCSS 0 0 0 0 Updated Jan 13, 2026
  • beebop Public

    Frontend code for beebop

    bacpop/beebop’s past year of commit activity
    TypeScript 1 0 4 5 Updated Jan 12, 2026
  • ggCaller Public

    Bifrost graph gene caller.

    bacpop/ggCaller’s past year of commit activity
    C++ 97 MIT 6 2 0 Updated Jan 9, 2026
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    bacpop/PopPUNK’s past year of commit activity
    Python 102 Apache-2.0 20 38 1 Updated Jan 9, 2026
  • beebop_py Public

    Python API for beebop

    bacpop/beebop_py’s past year of commit activity
    Python 0 0 0 5 Updated Jan 9, 2026
  • ska.rust Public

    Split k-mer analysis – version 2

    bacpop/ska.rust’s past year of commit activity
    Rust 103 Apache-2.0 8 10 1 Updated Jan 8, 2026
  • 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 1 Updated Jan 8, 2026
  • PopPIPE Public

    Population analysis PIPEline 🛠🧬

    bacpop/PopPIPE’s past year of commit activity
    Python 22 Apache-2.0 7 3 0 Updated Jan 5, 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 Jan 2, 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++ 3 Apache-2.0 1 0 0 Updated Dec 19, 2025
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