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sdsl-lite

Succinct Data Structure Library 2.0

sequencetubemap

displays multiple genomic sequences in the form of a tube map

sonlib

Small general purpose library for C and Python with focus on bioinformatics.

stream

compressed protobuf streaming C++ headers library

structures

A collection of c++ data structures I've coded up for various projects

sublinear-li-stephens

Calculates the probability of a haplotype given a population reference panel

superbubbles

SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.

sv-genotyping-paper

tabixpp

C++ wrapper to tabix indexer

toil-vg

Distributed and cloud computing framework for vg

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

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 :)

vg

tools for working with genome variation graphs

vg_biowulf

vg_ci_prebake

Prebaked Docker image to speed up VG CI

vg_docker

Contains dockerfiles that build the vgteam containers at our Dockerhub. Just add data!

vg_snakemake

Snakemake workflow for the vg toolkit.

vg_wdl

Workflow Description Language (WDL) scripts for common vg workflows

vgteam.github.io

vgteam Github page

vowpal_wabbit

Vowpal Wabbit is a machine learning system which pushes the frontier of machine learning with techniques such as online, hashing, allreduce, reductions, learning2search, active, and interactive learning.

wfa2-lib

WFA2-lib: Wavefront alignment algorithm library v2

xg

xg0: a simpler xg index

xg-old

succinct labeled graphs with collections and paths

yeastgraphs

Contains scripts for generating variant graphs for a whole bunch of yeast strains. Pan-genomics in every sense of the word.