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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 89 18

  2. pp-sketchlib pp-sketchlib Public

    Library of sketching functions used by PopPUNK

    C++ 30 7

  3. ggCaller ggCaller Public

    Bifrost graph gene caller.

    C++ 86 6

  4. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 57 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 89 Apache-2.0 18 20 3 Updated Sep 19, 2024
  • Pansim Public

    Pangenome simulator

    bacpop/Pansim’s past year of commit activity
    Rust 2 MIT 0 0 0 Updated Sep 19, 2024
  • sketchlib.rust Public

    Rust reimplementation of pp-sketchlib

    bacpop/sketchlib.rust’s past year of commit activity
    Rust 2 Apache-2.0 1 14 (4 issues need help) 1 Updated Sep 16, 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 Sep 12, 2024
  • beebop_py Public

    Python API for beebop

    bacpop/beebop_py’s past year of commit activity
    Python 0 0 0 4 Updated Sep 12, 2024
  • beebop Public

    Frontend code for beebop

    bacpop/beebop’s past year of commit activity
    CSS 1 0 0 3 Updated Sep 9, 2024
  • beebop-k8s Public
    bacpop/beebop-k8s’s past year of commit activity
    Shell 0 0 0 0 Updated Sep 5, 2024
  • beebop-deploy Public

    Deploy scripts for beebop

    bacpop/beebop-deploy’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 3, 2024
  • readfish Public Forked from LooseLab/readfish

    Read Until scripts with graph alignment

    bacpop/readfish’s past year of commit activity
    Python 1 GPL-3.0 34 0 0 Updated Aug 22, 2024
  • bacpop-website Public

    Code for group website

    bacpop/bacpop-website’s past year of commit activity
    HTML 0 Apache-2.0 4 0 0 Updated Aug 20, 2024
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