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    • Web interface for the sparrowhawk genome assembler using WebAssembly and Rust 🦅
      Vue
      0080Updated Aug 1, 2025Aug 1, 2025
    • Pansim

      Public
      Pangenome simulator
      Rust
      0200Updated Aug 1, 2025Aug 1, 2025
    • Negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
      R
      0000Updated Aug 1, 2025Aug 1, 2025
    • Fast sequence distance estimates
      Rust
      414110Updated Jul 31, 2025Jul 31, 2025
    • Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅
      Rust
      1990Updated Jul 29, 2025Jul 29, 2025
    • PopPUNK

      Public
      PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
      Python
      19100321Updated Jul 29, 2025Jul 29, 2025
    • Deploy scripts for beebop
      Python
      0000Updated Jul 29, 2025Jul 29, 2025
    • Code for group website
      HTML
      8100Updated Jul 29, 2025Jul 29, 2025
    • ska.rust

      Public
      Split k-mer analysis – version 2
      Rust
      68790Updated Jul 24, 2025Jul 24, 2025
    • Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
      Stan
      0500Updated Jul 17, 2025Jul 17, 2025
    • beebop_py

      Public
      Python API for beebop
      Python
      0003Updated Jul 7, 2025Jul 7, 2025
    • An R package for translating SBML models into odin models.
      R
      0100Updated Jun 20, 2025Jun 20, 2025
    • A viewer of odin.js models from the biomodels database
      JavaScript
      1260Updated Jun 20, 2025Jun 20, 2025
    • Mutation simulation to test ska.rust sensitivity
      Rust
      0100Updated Jun 12, 2025Jun 12, 2025
    • PopPIPE

      Public
      Population analysis PIPEline 🛠🧬
      Python
      62010Updated Apr 29, 2025Apr 29, 2025
    • Library of sketching functions used by PopPUNK
      C++
      831110Updated Mar 31, 2025Mar 31, 2025
    • beebop

      Public
      Frontend code for beebop
      TypeScript
      0103Updated Mar 18, 2025Mar 18, 2025
    • mandrake

      Public
      Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
      Python
      23840Updated Mar 7, 2025Mar 7, 2025
    • A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.
      HTML
      0100Updated Feb 18, 2025Feb 18, 2025
    • trees_rs

      Public
      Tree inference in rust
      Rust
      1160Updated Jan 6, 2025Jan 6, 2025
    • Methods to determine sequence element (unitig) presence/absence
      C++
      320130Updated Dec 6, 2024Dec 6, 2024
    • ggCaller

      Public
      Bifrost graph gene caller.
      C++
      69530Updated Sep 20, 2024Sep 20, 2024
    • Shell
      0000Updated Sep 5, 2024Sep 5, 2024
    • readfish

      Public
      Read Until scripts with graph alignment
      Python
      35100Updated Aug 22, 2024Aug 22, 2024
    • DATACIN

      Public
      Draw A Tree And Colour it IN
      Rust
      1140Updated Aug 5, 2024Aug 5, 2024
    • Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
      Python
      12430Updated Jul 22, 2024Jul 22, 2024
    • Scripts for adaptive sampling analysis
      R
      2300Updated Jul 3, 2024Jul 3, 2024
    • cgt

      Public
      Calculate sensible core gene thresholds for metagenomic data
      Rust
      0400Updated Feb 14, 2024Feb 14, 2024
    • This repo is for to summarise pubmed texts with a given gene/species query
      Python
      0000Updated Dec 11, 2023Dec 11, 2023
    • Python
      1000Updated Nov 27, 2023Nov 27, 2023