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• W4316369218 abstract "Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer’s and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of-the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT-based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies." @default.
• W4316369218 created "2023-01-16" @default.
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• W4316369218 date "2023-01-15" @default.
• W4316369218 modified "2023-09-27" @default.
• W4316369218 title "Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation" @default.
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• W4316369218 doi "https://doi.org/10.1101/2023.01.12.523790" @default.
• W4316369218 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36711673" @default.
• W4316369218 hasPublicationYear "2023" @default.
• W4316369218 type Work @default.
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