ArticleNature communications2024
A sequence-aware merger of genomic structural variations at population scale.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- A trio-based long-read sequencing workflow identifies a pathogenic transposable element insertion in a previously undiagnosed patient.Journal of human genetics · 2026Article
- Stepwise allelic trajectory of ETP2 underlies trade-off between UVB tolerance and submergence adaptation in Arabidopsis thaliana.Nature communications · 2026Article
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Bayesian Integrative Detection of Structural Variations With False Discovery Rate Control.Biometrical journal. Biometrische Zeitschrift · 2026Article
- Integrating pan-genome analysis, GWAS, and interpretable machine learning to prioritize trait-associated structural variations in Setaria italica.Plant communications · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant.Nature communications · 2026Article
- The pangenome enhances the understanding of the genetic diversity of papaya.Horticulture research · 2026Article
- SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets.Nucleic acids research · 2026Article
- OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.Bioinformatics (Oxford, England) · 2025Article
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data.BMC bioinformatics · 2025Article
- Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.BMC biology · 2025Article
- EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.Plant communications · 2025Article
- Genetic insights into developmental variations of spiny bracts among hazels through the pangenome construction.Plant biotechnology journal · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia.Molecular horticulture · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Merging structural variations (SVs) at the population level presents a significant challenge, yet it is essential for conducting comprehensive genotypic analyses, especially in the era of pangenomics. Here, we introduce PanPop, a tool that utilizes an advanced sequence-aware SV merging algorithm to efficiently merge SVs of various types. We demonstrate that PanPop can merge and optimize the majority of multiallelic SVs into informative biallelic variants. We show its superior precision and lower rates of missing data compared to alternative software solutions. Our approach not only enables the filtering of SVs by leveraging multiple SV callers for enhanced accuracy but also facilitates the accurate merging of large-scale population SVs. These capabilities of PanPop will help to accelerate future SV-related studies.
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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.