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46 search results found

tools for working with genome variation graphs

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

the pangenome graph builder

Ppanggolin ⭐ 191

Build a partitioned pangenome graph from microbial genomes

Rust Mdbg ⭐ 149

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

Px2graph ⭐ 113

Training code for "Pixels to Graphs by Associative Embedding"

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Python graph database framework for bioinformatics

Modular Multi-scale Integrated Genome Graph Browser

Minia is a short-read assembler based on a de Bruijn graph

Cuttlefish ⭐ 64

Building the compacted de Bruijn graph efficiently from references or reads.

Semantic Image Manipulation using Scene Graphs (CVPR 2020)

W2rap Contigger ⭐ 44

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

Metage2metabo ⭐ 42

From annotated genomes to metabolic screening in large scale microbiotas

Graph based multi genome aligner

Novograph ⭐ 36

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Graph Genomics Review ⭐ 35

Pangenome graphs (review article on graph-based pangenomic methods)

Gengraph ⭐ 34

A repository for the GenGraph toolkit for the creation and manipulation of graph genomes

A fuzzy Bruijn graph approach to long noisy reads assembly

Genomegraphs.jl ⭐ 29

A modern genomics framework for julia

Population Reference Graphs for the HLA and MHC.

Argweaver ⭐ 28

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

Knetminer ⭐ 25

KnetMiner - webapp to search and visualize genome-scale knowledge graphs

Blastfrost ⭐ 23

GRAph-based Finding of Individual Motif Occurrences

extract MSAs from genome variation graphs

Coursera_data_structures_and_algorithms_specialization ⭐ 16

My solution to Data Structures and Algorithms Specialization (Algorithmic Toolbox; Data Structures; Algorithms on Graphs; Algorithms on Strings; Advanced Algorithms and Complexity; Genome Assembly Programming Challenge)

Chromegcn ⭐ 16

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

Graph-aware Retrieval of Selective Sweeps

Debruijn ⭐ 14

de Bruijn graph construction tool

Coronavirus Knowledge Graph ⭐ 14

OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (new version: https://github.com/sbl-sdsc/coronavirus-knowledge-

Viral Assembly ⭐ 13

exploring viral genome assembly with variation graph tools

Two_step_graph_mapper ⭐ 12

A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers

MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.

De Bruijn graph construction for large k.

Distributed and cloud computing framework for vg

Pangenome_graphs ⭐ 9

Constructing pan genome graphs from "protein family" assignments

Play with The Reference Graph

Pgvf Spec ⭐ 9

Pangenome Graph Variation Format (PGVF)

Graph_summarization ⭐ 8

Browser for Graph Genomes built with VG based on Graph Summarization to provide semantic zoom. As a user zooms in on a graph genome, the topology becomes more complex. Provides visualization for variation within a species of plant or animal. Designed to scale up to thousands of specimens and provide useful visualizations.

Hgvm Graph Bakeoff Evaluations ⭐ 8

All code for reproducing reference graph bakeoff results

🧬 A multiple-genome graph visualizer for the JVM

Graph_peak_caller ⭐ 7

ChIP-seq peak caller for reads mapped to a graph-based reference genome

Genome Sequencing ⭐ 7

Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.

RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)

Corticall ⭐ 6

Germline DNM caller based on LdBG assembly of pathogens

Multi Genome Reference ⭐ 6

A program to generate a graph which presents a simplified representation of several full length genomes

Graph_extraction ⭐ 6

Virus_graphs ⭐ 6

Making Representative Genome Graphs from Eukaryotic Viruses and Phages

Genome Graph Japan

Abyss Scaffold Paper ⭐ 5

Scaffolding a genome sequence assembly using ABySS

visual analysis of your VCF files

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