ArticleNucleic acids research2021
Nebula: ultra-efficient mapping-free structural variant genotyper.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 28 citations in OpenAlex.
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- Article
- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- The Great Genotyper: a graph-based method for population genotyping of small and structural variants.GigaScience · 2025Article
- On weighted k-mer dictionaries.Algorithms for molecular biology : AMB · 2023Article
- SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.Nature methods · 2023Article
- Genetic Polymorphisms Associated with Perioperative Joint Infection following Total Joint Arthroplasty: A Systematic Review and Meta-Analysis.Antibiotics (Basel, Switzerland) · 2022Review
- Dysgu: efficient structural variant calling using short or long reads.Nucleic acids research · 2022Article
- Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data.BMC genomics · 2022Article
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
- Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs.The plant genome · 2022Review
- Population-scale genotyping of structural variation in the era of long-read sequencing.Computational and structural biotechnology journal · 2022Review
- Effective sequence similarity detection with strobemers.Genome research · 2021Article
- Comparative genome analysis using sample-specific string detection in accurate long reads.Bioinformatics advances · 2021Article
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task that requires extensive computational resources. Furthermore, current approaches are mostly limited to only specific types of variants and are generally prone to various errors and ambiguities when genotyping complex events. We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches. Our method Nebula utilizes the changes in the count of k-mers to predict the genotype of structural variants. We have shown that not only Nebula is an order of magnitude faster than mapping based approaches for genotyping structural variants, but also has comparable accuracy to state-of-the-art approaches. Furthermore, Nebula is a generic framework not limited to any specific type of event. Nebula is publicly available at https://github.com/Parsoa/Nebula.
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