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    69 repositories

    • povu

      Public
      A toolkit for exploring regions of variation in a variation graph
      C++
      •
      MIT License
      •2•11•3•0•Updated Aug 20, 2025Aug 20, 2025

    • allwave

      Public
      simple interface for all-way alignment with biWFA
      Rust
      •
      MIT License
      •0•2•0•8•Updated Aug 18, 2025Aug 18, 2025

    • impg

      Public
      implicit pangenome graph
      Rust
      •
      MIT License
      •6•67•0•2•Updated Aug 14, 2025Aug 14, 2025

    • genotypify

      Public
      Genotyping lots of samples with big pangenomes
      Python
      •
      MIT License
      •0•10•0•0•Updated Aug 11, 2025Aug 11, 2025

    • pggb

      Public
      the pangenome graph builder
      Shell
      •
      MIT License
      •45•444•50•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

    • odgi

      Public
      Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
      C++
      •
      MIT License
      •44•219•46•8•Updated Jul 24, 2025Jul 24, 2025

    • smoothxg

      Public
      linearize and simplify variation graphs using blocked partial order alignment
      C++
      •
      Other
      •8•58•7•2•Updated Jul 22, 2025Jul 22, 2025

    • seqrush

      Public
      online variation graph induction
      Rust
      •
      MIT License
      •1•9•0•1•Updated Jul 15, 2025Jul 15, 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

    • HPRCv2

      Public
      pangenome alignment, implicit/explicit graph, and variants for human pangenome project release 2
      MIT License
      •0•4•0•0•Updated Jul 7, 2025Jul 7, 2025

    • gafpack

      Public
      convert variation graph alignments to coverage maps over nodes
      Rust
      •
      MIT License
      •2•24•0•0•Updated Jun 24, 2025Jun 24, 2025

    • vcfbub

      Public
      use variant nesting information to flter overlapping sites from vg deconstruct output
      Rust
      •
      MIT License
      •2•26•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
      •3•1•0•0•Updated May 14, 2025May 14, 2025

    • pggb-workshop

      Public
      tutorial on pggb
      7•35•1•0•Updated Jan 13, 2025Jan 13, 2025

    • HumanPangenomeBYOD2024

      Public
      Material for the Human Pangenome Bring Your Own Data (BYOD) analysis Workshop 2024, October 21-25 in Cape Town, South Africa.
      MIT License
      •2•7•0•0•Updated Oct 29, 2024Oct 29, 2024

    • PanSN-spec

      Public
      Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
      2•39•4•1•Updated Oct 13, 2024Oct 13, 2024

    • lifetree

      Public
      hard mode all genomes alignment
      Shell
      •2•5•0•0•Updated Sep 3, 2024Sep 3, 2024

    • pggb-paper

      Public
      The PanGenome Graph Builder
      TeX
      •
      MIT License
      •2•16•0•0•Updated Jul 17, 2024Jul 17, 2024

    • MemPanG24

      Public
      Computational Pangenomics in Memphis
      HTML
      •
      MIT License
      •3•2•0•0•Updated Jul 11, 2024Jul 11, 2024

    • chromosome_communities

      Public
      Recombination between heterologous human acrocentric chromosomes
      recombinationpangenometranslocation
      R
      •0•6•0•0•Updated Jul 6, 2024Jul 6, 2024

    • sorting-paper

      Public
      Path-Guided Stochastic Gradient Descent layout of pangenome graphs
      TeX
      •
      MIT License
      •2•3•0•0•Updated May 5, 2024May 5, 2024

    • spodgi

      Public
      RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)
      sparqlgfaodgirdflibvariation-graphs
      Python
      •
      MIT License
      •4•11•9•0•Updated Mar 20, 2024Mar 20, 2024

    • keane_mouse_pangenome

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 20, 2024Mar 20, 2024

    • jbrowse-visualization

      Public
      Workflow to visualize pggb graphs in jbrowse
      Shell
      •0•9•0•0•Updated Mar 15, 2024Mar 15, 2024

    • mafchunk

      Public
      split MAF blocks into smaller chunks
      Rust
      •
      MIT License
      •0•4•0•0•Updated Mar 14, 2024Mar 14, 2024

    • tree_of_life_alignment

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 14, 2023Aug 14, 2023