Oxford Nanopore Ultra Long (UL) Whole Genome Sequencing of the GIAB HG008-T tumor cell line
Ultra-high molecular weight DNA was extracted from approximately five million non-viable HG008-T cells (batch 0823p23) utilizing New England Biolabs Monarch HMW DNA Extraction Kit for Cells (NEB #T3050).  Extraction yielded ~25-30 ug with DNA hundreds of kilobases long, with some exceeding megabases), as measured by preliminary analysis of ONT sequencing. A single library preparation was performed utilizing Oxford Nanopore Technologies Ultra-Long DNA Sequencing Kit Version 14 (SQK-ULK114) using all isolated gDNA. Nanopore based sequencing was performed on an Oxford Nanopore Technologies (ONT) 48/PromethION A-Series Data Acquisition Unit (PN: PRO-SEQ048/PRO-PRCAMP) utilizing ONTs ULK114 chemistry with the E8.2.1 motor protein and PromethION R10.4.1 Flow Cells (PN: FLO-PRO114M). Two flow cells were used and received a total of four library loads with three wash (ONT Flow Cell Wash Kit XL PN: EXP-WSH004-XL) and reload steps per flowcell. The Dorado v0.8.1 basecaller (https://github.com/nanoporetech/dorado) and the super accuracy (sup) model (v5.0.0), were used for basecalling, including 5mC_5hmC modification calls (v2.0.1). Basecalling successfully completed with no errors. Output from the basecaller is a bam file of unaligned reads including modified bases.