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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 Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Python 94 20

  2. pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 8

  3. ggCaller Public

    Bifrost graph gene caller.

    C++ 91 6

  4. ska.rust Public

    Split k-mer analysis – version 2

    Rust 73 5

  5. mandrake Public

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

    Python 36 2

  6. unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    C++ 18 3

Repositories

Showing 10 of 40 repositories
  • compartmental-models-odin-dust Public

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

    HTML 0 Apache-2.0 0 0 0 Updated Jan 17, 2025
  • ska.rust Public

    Split k-mer analysis – version 2

    Rust 73 Apache-2.0 5 7 1 Updated Jan 17, 2025
  • beebop Public

    Frontend code for beebop

    TypeScript 1 0 0 5 Updated Jan 16, 2025
  • beebop_py Public

    Python API for beebop

    Python 0 0 0 5 Updated Jan 16, 2025
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Python 94 Apache-2.0 20 26 2 Updated Jan 14, 2025
  • pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 Apache-2.0 8 11 0 Updated Jan 6, 2025
  • trees_rs Public

    Tree inference in rust

    Rust 1 AGPL-3.0 1 6 0 Updated Jan 6, 2025
  • bacpop-website Public

    Code for group website

    HTML 1 Apache-2.0 5 0 0 Updated Dec 12, 2024
  • sketchlib.rust Public

    Rust reimplementation of pp-sketchlib

    Rust 2 Apache-2.0 1 16 (4 issues need help) 0 Updated Dec 12, 2024
  • SBMLtoOdin Public

    An R package for translating SBML models into odin models.

    R 0 0 0 0 Updated Dec 9, 2024

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