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vgteam

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vgteam's repositories

vg

tools for working with genome variation graphs

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sequenceTubeMap

displays multiple genomic sequences in the form of a tube map

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giraffe-sv-paper

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gssw

efficient alignment of strings to partially ordered string graphs

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libbdsg

Optimized sequence graph implementations for graph genomics

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toil-vg

Distributed and cloud computing framework for vg

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libhandlegraph

Library for the Handle Graph abstraction

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vg_wdl

Workflow Description Language (WDL) scripts for common vg workflows

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GetBlunted

For bluntifying overlapped GFAs

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libvgio

A dynamic library that provides io for the vg toolkit.

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sdsl-lite

Succinct Data Structure Library 2.0

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vg_snakemake

Snakemake workflow for the vg toolkit.

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xg

xg0: a simpler xg index

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long-read-giraffe-experiments

Experimental materials for testing the long-read mapping abilities of vg giraffe

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DYNAMIC

Dynamic succinct/compressed data structures

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gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

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libsnarls

Library for working with variable sites in handle graphs

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structures

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

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vcflib

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

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Complete-Striped-Smith-Waterman-Library

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dind

Docker in Docker

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dozeu

SIMD-parallel BLAST X-drop DP on sequence graphs

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haplotype-aware-mapping-paper

Scripts for the haplotype-aware mapping paper project

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htslib

C library for high-throughput sequencing data formats

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libbdsg-easy

Easy installation for libbdsg

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sublinear-Li-Stephens

Calculates the probability of a haplotype given a population reference panel

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Superbubbles

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

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vg_ci_prebake

Prebaked Docker image to speed up VG CI

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WFA2-lib

WFA2-lib: Wavefront alignment algorithm library v2

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YeastGraphs

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

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