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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 97 20

  2. pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 8

  3. ggCaller Public

    Bifrost graph gene caller.

    C++ 93 6

  4. ska.rust Public

    Split k-mer analysis – version 2

    Rust 81 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++ 19 3

Repositories

Showing 10 of 40 repositories
  • sketchlib.rust Public

    Rust reimplementation of pp-sketchlib

    Rust 3 Apache-2.0 2 14 (1 issue needs help) 0 Updated Apr 4, 2025
  • Pansim Public

    Pangenome simulator

    Rust 2 MIT 0 0 0 Updated Apr 4, 2025
  • SBMLtoOdin Public

    An R package for translating SBML models into odin models.

    R 1 Apache-2.0 0 0 0 Updated Apr 4, 2025
  • TOMBOMBADIL Public

    Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci

    Stan 5 Apache-2.0 0 0 0 Updated Apr 3, 2025
  • pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 Apache-2.0 8 11 0 Updated Mar 31, 2025
  • PopPIPE Public

    Population analysis PIPEline 🛠🧬

    Python 16 Apache-2.0 6 1 0 Updated Mar 25, 2025
  • beebop_py Public

    Python API for beebop

    Python 0 0 0 3 Updated Mar 25, 2025
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Python 97 Apache-2.0 20 28 1 Updated Mar 24, 2025
  • beebop Public

    Frontend code for beebop

    TypeScript 1 0 0 3 Updated Mar 18, 2025
  • bacpop-website Public

    Code for group website

    HTML 1 Apache-2.0 7 0 0 Updated Mar 13, 2025
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