ArticleScience (New York, N.Y.)2021
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 252 papers, 1 of them a synthesis that pooled it.
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Who cites it
252 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GWAS meta-analysis using a graph-based pan-genome enhanced gene mining efficiency for agronomic traits in rice.Nature communications · 2025Pooled it
- Small variant calling in the era of long-read sequencing.Nature reviews. Genetics · 2026Review
- T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants.iScience · 2026Article
- 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
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- An Icelandic pangenome reference.Nature · 2026Article
- Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.Nature genetics · 2026Article
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Privacy-preserving pangenome graphs.Nature communications · 2026Article
- Defining and cataloging variants in pangenome graphs.Cell genomics · 2026Article
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Graph-based pangenomics reveals the genetic basis of agronomic traits in tomato fruits.Horticulture research · 2026Article
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- On the ancestry and evolution of the extinct dire wolf.Cell genomics · 2026Article
- A complete genome for the common marmoset.Cell · 2026Article
- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
192 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
We introduce Giraffe, a pangenome short-read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe maps sequencing reads to thousands of human genomes at a speed comparable to that of standard methods mapping to a single reference genome. The increased mapping accuracy enables downstream improvements in genome-wide genotyping pipelines for both small variants and larger structural variants. We used Giraffe to genotype 167,000 structural variants, discovered in long-read studies, in 5202 diverse human genomes that were sequenced using short reads. We conclude that pangenomics facilitates a more comprehensive characterization of variation and, as a result, has the potential to improve many genomic analyses.
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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.