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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 93 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++ 88 6

  4. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 71 4

  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

    Python 18 3

Repositories

Showing 10 of 40 repositories
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    bacpop/PopPUNK’s past year of commit activity
    Python 93 Apache-2.0 20 24 2 Updated Nov 25, 2024
  • beebop_py Public

    Python API for beebop

    bacpop/beebop_py’s past year of commit activity
    Python 0 0 0 5 Updated Nov 25, 2024
  • beebop Public

    Frontend code for beebop

    bacpop/beebop’s past year of commit activity
    TypeScript 1 0 0 4 Updated Nov 21, 2024
  • trees_rs Public

    Tree inference in rust

    bacpop/trees_rs’s past year of commit activity
    Rust 1 AGPL-3.0 0 3 0 Updated Nov 21, 2024
  • SBMLtoOdin Public

    An R package for translating SBML models into odin models.

    bacpop/SBMLtoOdin’s past year of commit activity
    R 0 0 0 0 Updated Nov 11, 2024
  • bacpop-website Public

    Code for group website

    bacpop/bacpop-website’s past year of commit activity
    HTML 1 Apache-2.0 5 0 0 Updated Nov 6, 2024
  • sketchlib.rust Public

    Rust reimplementation of pp-sketchlib

    bacpop/sketchlib.rust’s past year of commit activity
    Rust 2 Apache-2.0 1 16 (4 issues need help) 0 Updated Nov 4, 2024
  • ska.rust Public

    Split k-mer analysis – version 2

    bacpop/ska.rust’s past year of commit activity
    Rust 71 Apache-2.0 4 7 0 Updated Oct 29, 2024
  • 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 Oct 24, 2024
  • Pansim Public

    Pangenome simulator

    bacpop/Pansim’s past year of commit activity
    Rust 2 MIT 0 0 0 Updated Oct 17, 2024
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