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    79 repositories

    • seqwish

      Public
      alignment to variation graph inducer
      C++
      •
      MIT License
      •20•150•31•3•Updated Nov 8, 2025Nov 8, 2025

    • onecode-rs

      Public
      Rust bindings for ONEcode - a data representation format for genomic data
      C
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2025Nov 8, 2025

    • impg

      Public
      implicit pangenome graph
      Rust
      •
      MIT License
      •10•78•0•2•Updated Nov 8, 2025Nov 8, 2025

    • povu

      Public
      A toolkit for exploring regions of variation in a variation graph
      C++
      •
      MIT License
      •3•12•3•2•Updated Nov 7, 2025Nov 7, 2025

    • HPRCv2

      Public
      pangenome alignment, implicit/explicit graph, and variants for human pangenome project release 2
      R
      •
      MIT License
      •1•16•0•1•Updated Nov 7, 2025Nov 7, 2025

    • sweepga

      Public
      plane sweep filtering genome alignments
      Rust
      •
      MIT License
      •0•12•0•0•Updated Nov 7, 2025Nov 7, 2025

    • fastga-rs

      Public
      fastga rust library
      Rust
      •
      MIT License
      •0•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • alnviz

      Public
      Fast, interactive alignment viewer for pangenome analysis
      C
      •
      Other
      •0•3•0•0•Updated Nov 5, 2025Nov 5, 2025

    • iitree-rs

      Public
      Implicit Augmented Interval Tree (IAITree/cgranges) in Rust with memory-mapped disk storage
      Rust
      •0•1•0•0•Updated Nov 4, 2025Nov 4, 2025

    • gafpack

      Public
      convert variation graph alignments to coverage maps over nodes
      Rust
      •
      MIT License
      •2•26•0•0•Updated Nov 4, 2025Nov 4, 2025

    • allwave

      Public
      simple interface for all-way alignment with biWFA
      Rust
      •
      MIT License
      •0•2•0•9•Updated Nov 3, 2025Nov 3, 2025

    • genotypify

      Public
      Genotyping lots of samples with big pangenomes
      Python
      •
      MIT License
      •0•10•0•0•Updated Oct 30, 2025Oct 30, 2025

    • odgi

      Public
      Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
      C++
      •
      MIT License
      •43•226•54•8•Updated Oct 23, 2025Oct 23, 2025

    • seqrush

      Public
      online variation graph induction
      Rust
      •
      MIT License
      •1•11•0•0•Updated Oct 21, 2025Oct 21, 2025

    • impop

      Public
      Python
      •0•6•0•0•Updated Oct 19, 2025Oct 19, 2025

    • alnstat-rs

      Public
      Rust
      •0•1•0•0•Updated Oct 8, 2025Oct 8, 2025

    • HackPRC25

      Public
      Biohackathon following the HPRC25 conference
      HTML
      •0•1•0•0•Updated Oct 8, 2025Oct 8, 2025

    • seqwish-paper

      Public
      Unbiased pangenome graphs
      TeX
      •
      MIT License
      •0•3•0•0•Updated Oct 5, 2025Oct 5, 2025

    • lifetree

      Public
      hard mode all genomes alignment
      Shell
      •3•6•0•0•Updated Sep 25, 2025Sep 25, 2025

    • MemPanG26

      Public
      Computational Pangenomics in Memphis
      HTML
      •
      MIT License
      •4•1•0•0•Updated Sep 3, 2025Sep 3, 2025

    • pggb

      Public
      the pangenome graph builder
      Shell
      •
      MIT License
      •45•461•53•0•Updated Aug 3, 2025Aug 3, 2025

    • agc-rs

      Public
      agc rust bridge
      C++
      •
      MIT License
      •2•1•0•0•Updated Jul 31, 2025Jul 31, 2025

    • gfalace

      Public archive
      lace up GFA files using panSN path name sub-ranges to coordinate the lacing
      Rust
      •
      MIT License
      •1•12•2•1•Updated Jul 30, 2025Jul 30, 2025

    • smoothxg

      Public
      linearize and simplify variation graphs using blocked partial order alignment
      C++
      •
      Other
      •8•59•7•2•Updated Jul 22, 2025Jul 22, 2025

    • forgenom_summerschool2025

      Public
      PhD School on Modern Bioinformatics towards Pangenomics
      MIT License
      •0•0•0•0•Updated Jul 13, 2025Jul 13, 2025

    • poasta

      Public
      Fast and exact gap-affine partial order alignment
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • vcfbub

      Public
      use variant nesting information to flter overlapping sites from vg deconstruct output
      Rust
      •
      MIT License
      •2•29•2•1•Updated Jun 12, 2025Jun 12, 2025

    • manyfa

      Public
      bedtools getfasta / samtools faidx for pangenomes worth of FASTA files
      C++
      •0•7•0•0•Updated May 15, 2025May 15, 2025

    • MemPanG25

      Public
      Computational Pangenomics in Memphis
      HTML
      •
      MIT License
      •4•1•0•0•Updated May 14, 2025May 14, 2025

    • pggb-workshop

      Public
      tutorial on pggb
      7•36•1•0•Updated Jan 13, 2025Jan 13, 2025