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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 104 21

  2. ggCaller ggCaller Public

    Bifrost graph gene caller.

    C++ 98 6

  3. ska.rust ska.rust Public

    Split k-mer analysis – version 2

    Rust 104 8

  4. unitig-caller unitig-caller Public

    Methods to determine sequence element (unitig) presence/absence

    C++ 23 3

  5. PopPIPE PopPIPE Public

    Population analysis PIPEline 🛠🧬

    Python 22 7

  6. sketchlib.rust sketchlib.rust Public

    Fast sequence distance estimates

    Rust 26 6

Repositories

Showing 10 of 47 repositories
  • sparrowhawk Public

    Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅

    bacpop/sparrowhawk’s past year of commit activity
    Rust 11 Apache-2.0 2 10 0 Updated Mar 3, 2026
  • sparrowhawk-web Public

    Web interface for the sparrowhawk genome assembler using WebAssembly and Rust 🦅

    bacpop/sparrowhawk-web’s past year of commit activity
    Vue 1 Apache-2.0 1 8 0 Updated Mar 3, 2026
  • sketchlib.rust Public

    Fast sequence distance estimates

    bacpop/sketchlib.rust’s past year of commit activity
    Rust 26 Apache-2.0 6 14 0 Updated Mar 2, 2026
  • PopPUNK Public

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    bacpop/PopPUNK’s past year of commit activity
    Python 104 Apache-2.0 21 36 0 Updated Mar 2, 2026
  • Stubentiger Public

    An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations

    bacpop/Stubentiger’s past year of commit activity
    C++ 4 Apache-2.0 1 1 (1 issue needs help) 0 Updated Mar 2, 2026
  • PopPIPE Public

    Population analysis PIPEline 🛠🧬

    bacpop/PopPIPE’s past year of commit activity
    Python 22 Apache-2.0 7 2 0 Updated Mar 2, 2026
  • mgnify-wasm-preprocess Public

    Runs compression and indexing of fasta/gff files for jbrowse (in wasm)

    bacpop/mgnify-wasm-preprocess’s past year of commit activity
    Rust 1 0 0 0 Updated Mar 1, 2026
  • TOMBOMBADIL_jax Public

    JAX prototype of TOMBOMBADIL

    bacpop/TOMBOMBADIL_jax’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Feb 27, 2026
  • biomics_website Public

    Website for BIOMICS hackathon

    bacpop/biomics_website’s past year of commit activity
    SCSS 0 4 0 2 Updated Feb 26, 2026
  • TOMBOMBADIL Public

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

    bacpop/TOMBOMBADIL’s past year of commit activity
    Stan 5 Apache-2.0 0 0 0 Updated Feb 24, 2026
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