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    55 repositories

    • vg

      Public
      tools for working with genome variation graphs
      genomicsgraphdnavariation-graphgenome-graph
      C++
      •
      Other
      •215•1.3k•881•11•Updated Feb 3, 2026Feb 3, 2026

    • libbdsg

      Public
      Optimized sequence graph implementations for graph genomics
      C++
      •
      MIT License
      •6•34•24•9•Updated Feb 2, 2026Feb 2, 2026

    • long-read-giraffe-experiments

      Public
      Experimental materials for testing the long-read mapping abilities of vg giraffe
      Python
      •
      Other
      •2•5•20•0•Updated Jan 17, 2026Jan 17, 2026

    • libhandlegraph

      Public
      Library for the Handle Graph abstraction
      C++
      •
      MIT License
      •6•24•15•3•Updated Jan 15, 2026Jan 15, 2026

    • vg_ci_prebake

      Public
      Prebaked Docker image to speed up VG CI
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • sdsl-lite

      Public
      Succinct Data Structure Library 2.0
      C++
      •
      Other
      •356•10•0•1•Updated Jan 9, 2026Jan 9, 2026

    • libvgio

      Public
      A dynamic library that provides io for the vg toolkit.
      C++
      •
      Other
      •8•9•6•3•Updated Jan 8, 2026Jan 8, 2026

    • recombination-aware-giraffe-experiments

      Public
      Experimental materials for testing the recombination-aware mapping abilities of vg giraffe
      Python
      •
      Other
      •2•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • toil-vg

      Public
      Distributed and cloud computing framework for vg
      Python
      •
      Apache License 2.0
      •14•23•45•5•Updated Jan 6, 2026Jan 6, 2026

    • vg_wdl

      Public
      Workflow Description Language (WDL) scripts for common vg workflows
      WDL
      •
      MIT License
      •11•21•11•3•Updated Dec 15, 2025Dec 15, 2025

    • dind

      Public
      Docker in Docker
      Shell
      •
      Apache License 2.0
      •559•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • vg_snakemake

      Public
      Snakemake workflow for the vg toolkit.
      Python
      •
      GNU General Public License v3.0
      •6•11•0•1•Updated Nov 26, 2025Nov 26, 2025

    • sequenceTubeMap

      Public
      displays multiple genomic sequences in the form of a tube map
      JavaScript
      •
      MIT License
      •30•216•92•9•Updated Nov 12, 2025Nov 12, 2025

    • xg

      Public
      xg0: a simpler xg index
      C++
      •
      Other
      •4•5•6•2•Updated Nov 3, 2025Nov 3, 2025

    • vcflib

      Public
      a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
      C++
      •
      MIT License
      •226•1•0•1•Updated Jul 10, 2025Jul 10, 2025

    • fastahack

      Public
      utilities for indexing and sequence extraction from FASTA files
      C++
      •
      MIT License
      •25•1•0•0•Updated Jul 10, 2025Jul 10, 2025

    • BBHash

      Public
      Bloom-filter based minimal perfect hash function library
      C++
      •
      MIT License
      •32•2•0•0•Updated Jul 10, 2025Jul 10, 2025

    • DYNAMIC

      Public
      Dynamic succinct/compressed data structures
      C++
      •
      MIT License
      •24•1•0•0•Updated Apr 22, 2025Apr 22, 2025

    • libbdsg-easy

      Public
      Easy installation for libbdsg
      Makefile
      •2•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • sublinear-Li-Stephens

      Public
      Calculates the probability of a haplotype given a population reference panel
      C++
      •6•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • GetBlunted

      Public
      For bluntifying overlapped GFAs
      C++
      •0•13•5•1•Updated Jul 26, 2024Jul 26, 2024

    • dozeu

      Public
      SIMD-parallel BLAST X-drop DP on sequence graphs
      C
      •7•1•0•0•Updated May 30, 2024May 30, 2024

    • giraffe-sv-paper

      Public
      Shell
      •7•44•6•0•Updated May 8, 2024May 8, 2024

    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      •
      Other
      •460•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • WFA2-lib

      Public
      WFA2-lib: Wavefront alignment algorithm library v2
      C
      •
      Other
      •48•0•0•0•Updated Apr 25, 2023Apr 25, 2023

    • Complete-Striped-Smith-Waterman-Library

      Public
      C
      •121•0•0•1•Updated Dec 2, 2022Dec 2, 2022

    • haplotype-aware-mapping-paper

      Public
      Scripts for the haplotype-aware mapping paper project
      Shell
      •
      MIT License
      •0•0•1•0•Updated Sep 28, 2022Sep 28, 2022

    • structures

      Public
      A collection of c++ data structures I've coded up for various projects
      C++
      •
      Apache License 2.0
      •4•1•0•0•Updated Apr 28, 2022Apr 28, 2022

    • Superbubbles

      Public
      SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.
      C++
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Mar 6, 2022Mar 6, 2022

    • YeastGraphs

      Public
      Contains scripts for generating variant graphs for a whole bunch of yeast strains. Pan-genomics in every sense of the word.
      Jupyter Notebook
      •2•0•0•0•Updated Mar 6, 2022Mar 6, 2022