ArticleNature communications2024
Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data.
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 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Research evolution of flat peach (Frontiers in plant science · 2025Pooled it
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- SynFlow: an interactive online genome structural variant viewer.Bioinformatics (Oxford, England) · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic structural variation rescues a classic biological invader from a population bottleneck.Science advances · 2026Article
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- Article
- XtractPAV: an automated pipeline for identifying presence-absence variations across multiple genomes.BMC genomics · 2026Article
- 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
- Telomere-to-telomere genome assembly of the wood tiger moth Arctia plantaginis.Scientific data · 2026Article
- Long-read genomic analyses to elucidate hidden structural variations associated with MECP2 duplication syndrome.Journal of human genetics · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- A Murine Database of Structural Variants Identifies A Candidate Gene for a Spontaneous Murine Lymphoma Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Reference-Guided Chromosome-by-Chromosome de novo Assembly at Scale Using Low-Coverage High-Fidelity Long-Reads with HiFiCCL.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- Benchmarking major somatic structural variant callers on the HG008 genome.Frontiers in genetics · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Strawberry atlas:PeerJ · 2026Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational efficiency and lower coverage requirements, are prominent. Alternative approaches, relying solely on available reads for de novo genome assembly and employing assembly-based tools for SV detection via comparison to a reference genome, demand significantly more computational resources. However, the lack of comprehensive benchmarking constrains our comprehension and hampers further algorithm development. Here we systematically compare 14 read alignment-based SV calling methods (including 4 deep learning-based methods and 1 hybrid method), and 4 assembly-based SV calling methods, alongside 4 upstream aligners and 7 assemblers. Assembly-based tools excel in detecting large SVs, especially insertions, and exhibit robustness to evaluation parameter changes and coverage fluctuations. Conversely, alignment-based tools demonstrate superior genotyping accuracy at low sequencing coverage (5-10×) and excel in detecting complex SVs, like translocations, inversions, and duplications. Our evaluation provides performance insights, highlighting the absence of a universally superior tool. We furnish guidelines across 31 criteria combinations, aiding users in selecting the most suitable tools for diverse scenarios and offering directions for further method development.
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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.