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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 94 20

  2. pp-sketchlib pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 8

  3. ggCaller ggCaller Public

    Bifrost graph gene caller.

    C++ 91 6

  4. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 74 5

  5. mandrake mandrake Public

    Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

    Python 36 2

  6. unitig-caller unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    C++ 18 3

Repositories

Showing 10 of 40 repositories
  • beebop Public

    Frontend code for beebop

    bacpop/beebop’s past year of commit activity
    TypeScript 1 0 0 4 Updated Feb 5, 2025
  • beebop_py Public

    Python API for beebop

    bacpop/beebop_py’s past year of commit activity
    Python 0 0 0 4 Updated Feb 5, 2025
  • ska.rust Public

    Split k-mer analysis – version 2

    bacpop/ska.rust’s past year of commit activity
    Rust 74 Apache-2.0 5 6 1 Updated Feb 3, 2025
  • odinviewer Public

    A viewer of odin.js models from the biomodels database

    bacpop/odinviewer’s past year of commit activity
    JavaScript 1 MIT 1 1 1 Updated Feb 3, 2025
  • compartmental-models-odin-dust Public

    A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.

    bacpop/compartmental-models-odin-dust’s past year of commit activity
    HTML 0 Apache-2.0 0 0 0 Updated Jan 31, 2025
  • Pansim Public

    Pangenome simulator

    bacpop/Pansim’s past year of commit activity
    Rust 2 MIT 0 0 0 Updated Jan 31, 2025
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    bacpop/PopPUNK’s past year of commit activity
    Python 94 Apache-2.0 20 27 2 Updated Jan 29, 2025
  • sketchlib.rust Public

    Rust reimplementation of pp-sketchlib

    bacpop/sketchlib.rust’s past year of commit activity
    Rust 3 Apache-2.0 2 17 (4 issues need help) 0 Updated Jan 27, 2025
  • PopPIPE Public

    Population analysis PIPEline 🛠🧬

    bacpop/PopPIPE’s past year of commit activity
    Python 16 Apache-2.0 6 1 0 Updated Jan 23, 2025
  • pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    bacpop/pp-sketchlib’s past year of commit activity
    C++ 30 Apache-2.0 8 11 0 Updated Jan 6, 2025
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