{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kosugi S"],"funding":["Japan Society for the Promotion of Science"],"pagination":["246"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12366377"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["26(1)"],"pubmed_abstract":["Tandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed a computational tool, TRsv, to distinguish and detect TR-CNVs, SVs, and short indels using long reads. In evaluation with simulated and real datasets, TRsv outperformed existing tools for detection of TR-CNVs and indels and performed equally well for detection of SVs. We demonstrated genome-wide detection of TR-CNVs, including variants associated with gene expression, disease, and quantitative traits, using 160 long-read whole genome sequencing data and TRsv."],"journal":["Genome biology"],"pubmed_title":["TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data."],"pmcid":["PMC12366377"],"funding_grant_id":["JP21K06130","JP17K07264"],"pubmed_authors":["Kosugi S","Terao C"],"additional_accession":[]},"is_claimable":false,"name":"TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.","description":"Tandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed a computational tool, TRsv, to distinguish and detect TR-CNVs, SVs, and short indels using long reads. In evaluation with simulated and real datasets, TRsv outperformed existing tools for detection of TR-CNVs and indels and performed equally well for detection of SVs. We demonstrated genome-wide detection of TR-CNVs, including variants associated with gene expression, disease, and quantitative traits, using 160 long-read whole genome sequencing data and TRsv.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-05-29T17:06:21.295Z","creation":"2026-04-08T05:25:26.534Z"},"accession":"S-EPMC12366377","cross_references":{"pubmed":["40830527"],"doi":["10.1186/s13059-025-03718-z"]}}