Alignment of NA12884 HiFi reads to GRCh38
High molecular weight DNA was isolated using the Monarch® HMW DNA Extraction Kit for Cells & Blood (New England Biolabs, T3050L). DNA quantification was carried out using Qubit dsDNA HS (ThermoFisher, Q32854) on a DS-11 FX fluorometer (Denovix), and size distribution was checked with FEMTO Pulse (Agilent, M5330AA & FP-1002-0275). The DNA was sheared to the desired fragment size using the Megaruptor 3 (Diagenode, B06010003 & E07010003). PacBio HiFi libraries were generated using the SMRTbell prep kit 3.0 (PacBio, 102-182-700). Size selection was performed with diluted AMPure PB beads or using Pippin HT, with a high-pass cutoff between 10–17 kbp depending on the shear size (Sage Science, HTP0001 & HPE7510). Libraries were sequenced on the PacBio Revio platform with Revio SMRT Cells (PacBio, 102-202-200) and the Revio polymerase kit v1 (PacBio, 102-817-600), with a 2-hour pre-extension and 24-hour movie runtime. HiFi data were processed with the human-WGS-WDL (https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v1.0.3) to produce the haplotagged BAM files aligned to GRCh38.