ArticleGenome biology2020
VALOR2: characterization of large-scale structural variants using linked-reads.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of food-grade soybean.Frontiers in plant science · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.BMC bioinformatics · 2023Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods.Genes · 2022Article
- A robust benchmark for detection of germline large deletions and insertions.Nature biotechnology · 2020Article
- VALOR2: characterization of large-scale structural variants using linked-reads.Genome biology · 2020Article
- Resolving the full spectrum of human genome variation using Linked-Reads.Genome research · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.
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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.