High Coverage, Ultra-long Read Sequencing of Human Genomes
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The long reads and improved data throughput enabled by the Oxford Nanopore platform have enabled many genomic analyses, including detection of SVs and de novo genome assembly. Here, we describe the use of GridIONs to generate high coverage human genome sequences of three individuals from the 1000 Genomes Project selected by the Human Genome Structural Variation Consortium for comprehensive haplotype-aware structural variation detection. To exploit Nanopore’s potential of long read length and sequencing yield, we optimized protocols for preparing high-molecular weight genomic DNA library. Notably, we achieved multi-Gigabases (Gb) of reads of hundreds of kb of aligned sequences per run. To take advantage of the GridION highly parallel nature, we further built an efficient sample-to-data generation workflow and streamlined the data storage and QC pipeline. A single human genome of 30X coverage could be completed in two and a half weeks. With the high coverage Nanopore data from the wellcharacterized human genomes, we report the characterization and standardization of Oxford Nanopore performance matrices based on the latest technology updates.