ArticleNature methods2024
Personalized pangenome references.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- GBZ-base and GAF-base: Indexed pangenome file formats.bioRxiv : the preprint server for biology · 2026Article
- Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Article
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery.Nature communications · 2025Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Advancements in Animal Breeding: From Mendelian Genetics to Machine Learning.International journal of molecular sciences · 2025Review
- 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
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.bioRxiv : the preprint server for biology · 2025Article
- PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Pangenomes reduce reference bias by representing genetic diversity better than a single reference sequence. Yet when comparing a sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with by filtering rare variants. However, this blunt heuristic both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach that imputes a personalized pangenome subgraph by sampling local haplotypes according to k-mer counts in the reads. We implement the approach in the vg toolkit ( https://github.com/vgteam/vg ) for the Giraffe short-read aligner and compare its accuracy to state-of-the-art methods using human pangenome graphs from the Human Pangenome Reference Consortium. This reduces small variant genotyping errors by four times relative to the Genome Analysis Toolkit and makes short-read structural variant genotyping of known variants competitive with long-read variant discovery methods.
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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.