{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Magner R"],"funding":["NICHD NIH HHS","NIH HHS"],"pubmed_abstract":["We introduce blend-seq, a workflow for combining data from traditional short-read sequencing pipelines with low-coverage long reads, to improve variant discovery for single samples without the full cost of high-coverage long reads. We demonstrate that with only 4x long-read coverage augmenting 30x short reads, we can improve SNP discovery across the genome, exceeding performance beyond even high-coverage short reads (60x). For genotype-agnostic discovery of structural variants, we see a threefold improvement in recall while maintaining precision by using the low-coverage long reads on their own, and show how we can improve genotyping accuracy by adding in the short-read data. In addition, we demonstrate how the long reads can better phase these variants, incorporating long-context informat"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2024.11.01.621515"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12424989"],"repository":["biostudies-literature"],"pubmed_title":["Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery."],"pmcid":["PMC12424989"],"funding_grant_id":["U24 HD090743","OT2 OD038121"],"pubmed_authors":["Lennon N","Saponas S","Basu S","Shand M","Paulsen R","Cunial F","Magner R","Banks E"],"additional_accession":[]},"is_claimable":false,"name":"Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.","description":"We introduce blend-seq, a workflow for combining data from traditional short-read sequencing pipelines with low-coverage long reads, to improve variant discovery for single samples without the full cost of high-coverage long reads. We demonstrate that with only 4x long-read coverage augmenting 30x short reads, we can improve SNP discovery across the genome, exceeding performance beyond even high-coverage short reads (60x). For genotype-agnostic discovery of structural variants, we see a threefold improvement in recall while maintaining precision by using the low-coverage long reads on their own, and show how we can improve genotyping accuracy by adding in the short-read data. In addition, we demonstrate how the long reads can better phase these variants, incorporating long-context informat","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-05-26T17:03:35.384Z","creation":"2026-05-26T03:06:12.738Z"},"accession":"S-EPMC12424989","cross_references":{"pubmed":["40950019"],"doi":["10.1101/2024.11.01.621515"]}}