ArticleNature biotechnology2024
Detection of mosaic and population-level structural variants with Sniffles2.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 352 papers.
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Who cites it
352 citing papers in PubMed.
- Nanopore sequencing combined with adaptive sampling and NanoExpansion enables accurate characterization of repeat expansion disorders.NAR genomics and bioinformatics · 2026Article
- Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data.Quantitative biology (Beijing, China) · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- Long-read sequencing enables high-accuracy mitochondrial heteroplasmy detection in Parkinson's disease.BMC genomics · 2026Article
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- "NanoDel": identification of large-scale mitochondrial DNA deletions using long-read sequencing.Bioinformatics (Oxford, England) · 2026Article
- A trio-based long-read sequencing workflow identifies a pathogenic transposable element insertion in a previously undiagnosed patient.Journal of human genetics · 2026Article
- Structural variant calling using Sniffles2.Nature protocols · 2026Review
- Detecting pathogenic structural variation in families with undiagnosed rare disease in a national genome project.European journal of human genetics : EJHG · 2026Article
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Unified long-read panel for Parkinson's and repeat expansion disorders.NPJ Parkinson's disease · 2026Article
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Cost-efficient long-read trio-barcoded adaptive sequencing improves rare disease diagnosis.Nature communications · 2026Article
- Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.G3 (Bethesda, Md.) · 2026Article
- Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast.Genome biology and evolution · 2026Article
- Article
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
292 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
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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.