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@bacpop Bacterial population genetics

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    57 repositories

    • sparrowhawk-asm

      Public
      Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅
      rustbioinformaticswebassembly
      rustbioinformaticswebassemblygenome-assembly
      Rust
      ���
      Apache License 2.0
      •2•16•9•0•Updated Sep 30, 2026Sep 30, 2026

    • TOMBOMBADIL

      Public
      Rapid dN/dS calculation from codon alignments
      bioinformaticsgenomicsevolutionary-biology
      bioinformaticsgenomicsevolutionary-biology
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 29, 2026Sep 29, 2026

    • ALLCAPS

      Public
      Developing AI tools to analyse pneumococcal capsular biosynthetic loci, the primary target of Pneumococcal Conjugate Vaccines (PCVs).
      Python
      •
      MIT License
      •0•2•1•0•Updated Sep 22, 2026Sep 22, 2026

    • sparrowhawk-graph

      Public
      Crate to work with de Bruijn graphs on Rust, using petgraph
      bioinformaticsgenomicsgraph
      bioinformaticsgenomicsgraphwasm
      Rust
      •0•0•2•0•Updated Sep 21, 2026Sep 21, 2026

    • NFDS_Model

      Public
      Negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 21, 2026Sep 21, 2026

    • pangenomerge

      Public
      Python
      •
      MIT License
      •3•6•0•0•Updated Sep 13, 2026Sep 13, 2026

    • Menelmacar

      Public
      A viewer of odin.js models from the biomodels database
      JavaScript
      •
      MIT License
      •1•5•6•0•Updated Sep 2, 2026Sep 2, 2026

    • sparrowhawk

      Public
      In-browser tools for bacterial genome analysis 🦅
      Vue
      •
      Apache License 2.0
      •1•11•4•0•Updated Aug 31, 2026Aug 31, 2026

    • ggCaller

      Public
      Bifrost graph gene caller.
      C++
      •
      MIT License
      •6•102•6•0•Updated Aug 31, 2026Aug 31, 2026

    • ALLCAPS_Benchmark

      Public
      Nextflow
      •0•0•0•0•Updated Aug 27, 2026Aug 27, 2026

    • sketchlib.rust

      Public
      Fast sequence distance estimates
      bioinformaticsgenomicssketching
      bioinformaticsgenomicssketchingk-mer
      Rust
      •
      Apache License 2.0
      •7•34•16•1•Updated Aug 24, 2026Aug 24, 2026

    • mandrake.rust

      Public
      rust port of the mandrake (stochastic cluster embedding) algorithm
      Rust
      •
      Apache License 2.0
      •0•3•0•0•Updated Aug 21, 2026Aug 21, 2026

    • poppunk.rust

      Public
      rust reimplementation of PopPUNK
      Rust
      •
      Apache License 2.0
      •0•1•1•0•Updated Aug 21, 2026Aug 21, 2026

    • sparrowhawk-amr

      Public
      AMR detection, WebAssembly ready, and AMRFinderPlus DB-compatible, on Rust
      Rust
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • mandrake

      Public
      Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
      genomicsgpucuda
      genomicsgpucudaembeddingpathogens
      Python
      •
      Apache License 2.0
      •2•41•4•0•Updated Aug 7, 2026Aug 7, 2026

    • GHOST

      Public
      R
      •
      MIT License
      •0•1•1•0•Updated Aug 5, 2026Aug 5, 2026

    • pan-no-rec

      Public
      Rust bindings to find outlying pairwise gene distances in panaroo output
      Rust
      •0•0•1•0•Updated Jul 30, 2026Jul 30, 2026

    • bacpop-website

      Public
      Code for group website
      bioinformaticsmodellingbacteria
      bioinformaticsmodellingbacteriapopulation-genetics
      HTML
      •
      Apache License 2.0
      •10•1•0•0•Updated Jul 20, 2026Jul 20, 2026

    • ska.rust

      Public
      Split k-mer analysis – version 2
      rustbioinformaticsalignment
      rustbioinformaticsalignmentsequencek-merska
      Rust
      •
      Apache License 2.0
      •8•106•13•0•Updated Jul 9, 2026Jul 9, 2026

    • pp-sketchlib

      Public
      Library of sketching functions used by PopPUNK
      C++
      •
      Apache License 2.0
      •8•29•12•0•Updated Jun 8, 2026Jun 8, 2026

    • PopPUNK

      Public
      PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
      genomicssketchingbacteria
      genomicssketchingbacteriak-merpopulation-genetics
      Python
      •
      Apache License 2.0
      •23•112•42•1•Updated Jun 2, 2026Jun 2, 2026

    • cgt

      Public
      Calculate sensible core gene thresholds for metagenomic data
      Rust
      •
      Apache License 2.0
      •0•3•0•0•Updated Jun 1, 2026Jun 1, 2026

    • BacPrune-Rust

      Public
      Rust
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 18, 2026May 18, 2026

    • biomics_website

      Public
      Website for BIOMICS hackathon
      SCSS
      •4•0•0•1•Updated Apr 9, 2026Apr 9, 2026

    • Stubentiger

      Public
      An R package for a negative frequency-dependent selection (NFDS) model to describe vaccine type replacement in Streptococcus pneumoniae populations
      C++
      •
      Apache License 2.0
      •1•5•1•0•Updated Mar 19, 2026Mar 19, 2026

    • unitig-caller

      Public
      Methods to determine sequence element (unitig) presence/absence
      C++
      •
      Apache License 2.0
      •3•28•13•0•Updated Mar 6, 2026Mar 6, 2026

    • PopPIPE

      Public
      Population analysis PIPEline 🛠🧬
      Python
      •
      Apache License 2.0
      •7•28•2•0•Updated Mar 2, 2026Mar 2, 2026

    • mgnify-wasm-preprocess

      Public
      Runs compression and indexing of fasta/gff files for jbrowse (in wasm)
      Rust
      •0•2•0•0•Updated Mar 1, 2026Mar 1, 2026

    • TOMBOMBADIL.stan

      Public
      Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
      Stan
      •
      Apache License 2.0
      •0•6•0•0•Updated Feb 24, 2026Feb 24, 2026

    • beebop

      Public
      Frontend code for beebop
      TypeScript
      •
      Other
      •0•2•4•0•Updated Feb 24, 2026Feb 24, 2026
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