vgteam

Repositories

• vg

  tools for working with genome variation graphs

  genomics graph dna variation-graph genome-graph
  C++ 124 612 470 (9 issues need help) 6 Updated Mar 12, 2020

• handlegraph-paper

  the handle graph API implementation comparison paper
  TeX 1 0 0 1 Updated Mar 12, 2020

• odgi

  optimized dynamic genome graph implementation
  C++ MIT 10 32 12 2 Updated Mar 11, 2020

• vg_snakemake

  Snakemake workflow for the vg toolkit.
  Python GPL-3.0 0 1 0 0 Updated Mar 11, 2020

• toil-vg

  Distributed and cloud computing framework for vg
  Python Apache-2.0 6 5 37 (1 issue needs help) 2 Updated Mar 10, 2020

• vg_docker

  Contains dockerfiles that build the vgteam containers at our Dockerhub. Just add data!
  Shell MIT 2 3 5 2 Updated Feb 27, 2020

• vg_wdl

  Workflow Description Language (WDL) scripts for common vg workflows
  wdl MIT 3 4 4 0 Updated Feb 18, 2020

• graph-genomics-review

  Pangenome graphs (review article on graph-based pangenomic methods)
  TeX 10 30 0 0 Updated Feb 13, 2020

• libbdsg

  Optimized sequence graph implementations for graph genomics
  C++ MIT 2 7 5 1 Updated Feb 12, 2020

• libvgio

  A dynamic library that provides io for the vg toolkit.
  C++ 0 2 1 0 Updated Jan 15, 2020

• xg

  xg0: a simpler xg index
  C++ 4 2 4 2 Updated Jan 15, 2020

• libhandlegraph

  Library for the Handle Graph abstraction
  C++ MIT 1 7 10 3 Updated Jan 14, 2020

• dind

  Forked from jpetazzo/dind

  Docker in Docker
  Shell Apache-2.0 495 0 0 0 Updated Jan 3, 2020

• vg_ci_prebake

  Prebaked Docker image to speed up VG CI
  Dockerfile MIT 0 0 0 0 Updated Jan 3, 2020

• sequenceTubeMap

  displays multiple genomic sequences in the form of a tube map
  JavaScript MIT 12 88 38 5 Updated Dec 28, 2019

• structures

  Forked from jeizenga/structures

  A collection of c++ data structures I've coded up for various projects
  C++ Apache-2.0 3 0 0 0 Updated Dec 10, 2019

• gssw

  efficient alignment of strings to partially ordered string graphs
  C 13 21 2 1 Updated Dec 10, 2019

• sv-genotyping-paper
  Python MIT 1 9 1 0 Updated Nov 26, 2019

• BBHash

  Forked from rizkg/BBHash

  Bloom-filter based minimal perfect hash function library
  C++ MIT 20 1 0 0 Updated Nov 2, 2019

• GFA-spec

  Forked from GFA-spec/GFA-spec

  Graphical Fragment Assembly (GFA) Format Specification
  Makefile 23 0 0 0 Updated Oct 8, 2019

• libbdsg-easy

  Easy installation for libbdsg
  Makefile 1 0 0 0 Updated Sep 27, 2019

• gfakluge

  Forked from edawson/gfakluge

  A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
  C++ MIT 16 1 0 1 Updated Sep 18, 2019

• Veguns

  This a CWL workflow to turn bacterial genomes from ensembl into a VG pangenome variation graph. And connects it to the protein world of UniProt :)
  Common Workflow Language MIT 3 3 0 0 Updated Sep 10, 2019

• htslib

  Forked from samtools/htslib

  C library for high-throughput sequencing data formats
  C 328 0 0 0 Updated Sep 9, 2019

• vcflib

  Forked from vcflib/vcflib

  a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
  C++ MIT 173 0 0 1 Updated Sep 3, 2019

• DYNAMIC

  Forked from xxsds/DYNAMIC

  Dynamic succinct/compressed data structures
  C++ MIT 11 0 0 0 Updated Jul 23, 2019

• sonLib

  Forked from benedictpaten/sonLib

  Small general purpose library for C and Python with focus on bioinformatics.
  C MIT 23 0 0 0 Updated Jul 22, 2019

• ips4o

  Forked from SaschaWitt/ips4o

  In-place Parallel Super Scalar Samplesort (IPS⁴o)
  C++ BSD-2-Clause 7 0 0 0 Updated Jun 18, 2019

• raptor

  Forked from dajobe/raptor

  Redland Raptor RDF syntax library
  C 43 0 0 0 Updated Jun 5, 2019

• handle_paper
  TeX 0 0 0 0 Updated May 3, 2019