ArticleBioinformatics (Oxford, England)2020
Haplotype-aware graph indexes.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- A Run-Length-Compressed Skiplist Data Structure for Dynamic GBWTs Supports Time- and Space-Efficient Pangenome Operations over Syncmers.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- GBZ-base and GAF-base: Indexed pangenome file formats.bioRxiv : the preprint server for biology · 2026Article
- Using pangenome variation graphs to improve mutation detection in a large DNA virus.Microbial genomics · 2026Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.Research square · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.bioRxiv : the preprint server for biology · 2025Article
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- Accurate short-read alignment throughGenome research · 2025Article
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Gastric cancer genomics study using reference human pangenomes.Life science alliance · 2025Article
- Haplotype Matching with GBWT for Pangenome Graphs.bioRxiv : the preprint server for biology · 2025Article
- methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.Nucleic acids research · 2025Article
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- GIN-TONIC: non-hierarchical full-text indexing for graph genomes.NAR genomics and bioinformatics · 2024Article
- Personalized pangenome references.Nature methods · 2024Article
- Haplotype-aware sequence alignment to pangenome graphs.Genome research · 2024Article
- A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline.Genome biology · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationThe variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.
resultsWe augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes. AVAILABILITY AND IMPLEMENTATION: Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.