ArticleNature communications2025
K-mer analysis of long-read alignment pileups for structural variant genotyping.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Cost-efficient long-read trio-barcoded adaptive sequencing improves rare disease diagnosis.Nature communications · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease.bioRxiv : the preprint server for biology · 2026Article
- A systematic assessment of machine learning for structural variant filtering.bioRxiv : the preprint server for biology · 2026Article
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 2026Article
- First Insights into Ploidy and Genome Size Estimation inPlants (Basel, Switzerland) · 2025Article
- Population-scale Long-read Sequencing in themedRxiv : the preprint server for health sciences · 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
- Pangenome discovery of missing autism variants.medRxiv : the preprint server for health sciences · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Challenges in structural variant calling in low-complexity regions.GigaScience · 2025Article
- SVUPP: Pre-phasing long reads improves structural variant genotyping.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. Benchmarking against the latest SV datasets shows kanpig achieves a single-sample genotyping concordance of 82.1%, significantly outperforming existing tools, which average 66.3%. We explore kanpig's use for multi-sample projects by testing on 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), and produces higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample's 20x long-reads and can be run on PacBio or Oxford Nanopore long-reads.
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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.