Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

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 to be difficult inside homo

SUBMITTER: Kolmogorov M 

PROVIDER: S-EPMC9882142 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature