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    62 repositories

    • gafpack

      Public
      convert variation graph alignments to coverage maps over nodes
      Rust
      •
      MIT License
      •1•21•0•0•Updated Nov 14, 2024Nov 14, 2024

    • odgi

      Public
      Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
      C++
      •
      MIT License
      •40•194•42•7•Updated Nov 6, 2024Nov 6, 2024

    • impg

      Public
      implicit pangenome graph
      Rust
      •
      MIT License
      •5•43•2•1•Updated Nov 4, 2024Nov 4, 2024

    • pggb

      Public
      the pangenome graph builder
      Shell
      •
      MIT License
      •44•393•34•0•Updated Nov 1, 2024Nov 1, 2024

    • 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
      •1•7•0•0•Updated Oct 29, 2024Oct 29, 2024

    • genotypify

      Public
      Genotyping lots of samples with big pangenomes
      MIT License
      •0•5•0•0•Updated Oct 29, 2024Oct 29, 2024

    • smoothxg

      Public
      linearize and simplify variation graphs using blocked partial order alignment
      C++
      •
      Other
      •7•56•8•3•Updated Oct 15, 2024Oct 15, 2024

    • PanSN-spec

      Public
      Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
      1•32•3•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

    • povu

      Public
      C++
      •
      MIT License
      •1•10•1•0•Updated Aug 13, 2024Aug 13, 2024

    • pggb-paper

      Public
      The PanGenome Graph Builder
      TeX
      •
      MIT License
      •1•13•0•0•Updated Jul 17, 2024Jul 17, 2024

    • MemPanG24

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

    • chromosome_communities

      Public
      Recombination between heterologous human acrocentric chromosomes
      recombinationpangenometranslocation
      R
      •0•5•0•0•Updated Jul 6, 2024Jul 6, 2024

    • vcfbub

      Public
      use variant nesting information to flter overlapping sites from vg deconstruct output
      Rust
      •
      MIT License
      •1•23•2•1•Updated Jun 21, 2024Jun 21, 2024

    • MemPanG25

      Public
      Computational Pangenomics in Memphis
      HTML
      •
      MIT License
      •2•0•0•0•Updated May 22, 2024May 22, 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

    • gfalace

      Public
      lace up GFA files using panSN path name sub-ranges to coordinate the lacing
      Rust
      •
      MIT License
      •0•4•1•0•Updated Mar 14, 2024Mar 14, 2024

    • pggb-workshop

      Public
      tutorial on pggb
      5•26•1•0•Updated Jan 13, 2024Jan 13, 2024

    • tree_of_life_alignment

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

    • flubble

      Public
      finding single-entry single-exit bubbles in the flowgraph
      Rust
      •0•1•0•0•Updated Aug 11, 2023Aug 11, 2023

    • seqwish-paper

      Public
      Unbiased pangenome graphs
      TeX
      •
      MIT License
      •0•3•0•0•Updated Jun 28, 2023Jun 28, 2023

    • pangenome.github.io

      Public
      HTML
      •2•9•0•0•Updated Jun 13, 2023Jun 13, 2023

    • MemPanG23

      Public
      Computational Pangenomics in Memphis
      HTML
      •
      MIT License
      •2•7•0•0•Updated Jun 12, 2023Jun 12, 2023

    • HPRCyear1v2genbank

      Public
      building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
      Shell
      •1•14•1•0•Updated Feb 13, 2023Feb 13, 2023

    • gfagino

      Public
      your friendly pangenome graph genotyper
      Rust
      •0•10•0•0•Updated Feb 6, 2023Feb 6, 2023

    • rs-peanut

      Public
      GAF alignment evaluation tool.
      Rust
      •
      MIT License
      •0•4•0•0•Updated Nov 7, 2022Nov 7, 2022