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    54 repositories

    • vg

      Public
      tools for working with genome variation graphs
      genomicsgraphdnavariation-graphgenome-graph
      C++
      •
      Other
      •195•1.1k•837•8•Updated Jan 8, 2025Jan 8, 2025

    • long-read-giraffe-experiments

      Public
      Experimental materials for testing the long-read mapping abilities of vg giraffe
      Python
      •
      Other
      •0•4•18•0•Updated Jan 7, 2025Jan 7, 2025

    • vcflib

      Public
      a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
      C++
      •
      MIT License
      •221•1•0•1•Updated Jan 6, 2025Jan 6, 2025

    • libbdsg

      Public
      Optimized sequence graph implementations for graph genomics
      C++
      •
      MIT License
      •5•34•23•7•Updated Dec 18, 2024Dec 18, 2024

    • libhandlegraph

      Public
      Library for the Handle Graph abstraction
      C++
      •
      MIT License
      •6•23•15•2•Updated Dec 17, 2024Dec 17, 2024

    • libvgio

      Public
      A dynamic library that provides io for the vg toolkit.
      C++
      •
      Other
      •7•8•6•1•Updated Dec 16, 2024Dec 16, 2024

    • libbdsg-easy

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

    • sequenceTubeMap

      Public
      displays multiple genomic sequences in the form of a tube map
      JavaScript
      •
      MIT License
      •27•186•84•9•Updated Nov 20, 2024Nov 20, 2024

    • toil-vg

      Public
      Distributed and cloud computing framework for vg
      Python
      •
      Apache License 2.0
      •14•21•45•6•Updated Nov 5, 2024Nov 5, 2024

    • sdsl-lite

      Public
      Succinct Data Structure Library 2.0
      C++
      •
      Other
      •349•8•0•1•Updated Nov 4, 2024Nov 4, 2024

    • vg_wdl

      Public
      Workflow Description Language (WDL) scripts for common vg workflows
      WDL
      •
      MIT License
      •9•19•10•2•Updated Oct 30, 2024Oct 30, 2024

    • sublinear-Li-Stephens

      Public
      Calculates the probability of a haplotype given a population reference panel
      C++
      •7•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • vg_snakemake

      Public
      Snakemake workflow for the vg toolkit.
      Python
      •
      GNU General Public License v3.0
      •4•8•0•0•Updated Sep 30, 2024Sep 30, 2024

    • GetBlunted

      Public
      For bluntifying overlapped GFAs
      C++
      •0•13•4•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•42•6•0•Updated May 8, 2024May 8, 2024

    • xg

      Public
      xg0: a simpler xg index
      C++
      •
      Other
      •4•5•6•1•Updated Apr 22, 2024Apr 22, 2024

    • htslib

      Public
      C library for high-throughput sequencing data formats
      C
      •
      Other
      •443•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • vg_ci_prebake

      Public
      Prebaked Docker image to speed up VG CI
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2023Jun 18, 2023

    • dind

      Public
      Docker in Docker
      Shell
      •
      Apache License 2.0
      •559•0•0•0•Updated Jun 18, 2023Jun 18, 2023

    • WFA2-lib

      Public
      WFA2-lib: Wavefront alignment algorithm library v2
      C
      •
      Other
      •38•0•0•0•Updated Apr 25, 2023Apr 25, 2023

    • Complete-Striped-Smith-Waterman-Library

      Public
      C
      •116•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

    • libsnarls

      Public
      Library for working with variable sites in handle graphs
      C++
      •
      MIT License
      •1•1•0•0•Updated Mar 4, 2022Mar 4, 2022

    • gssw

      Public
      efficient alignment of strings to partially ordered string graphs
      C
      •17•33•2•2•Updated Jan 31, 2022Jan 31, 2022

    • gfakluge

      Public
      A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
      C++
      •
      MIT License
      •20•1•0•0•Updated Oct 4, 2021Oct 4, 2021

    • DYNAMIC

      Public
      Dynamic succinct/compressed data structures
      C++
      •
      MIT License
      •21•1•0•0•Updated Jul 12, 2021Jul 12, 2021