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bioRxiv · 10.1101/2023.06.06.543940

High Coverage Highly Accurate Long-Read Sequencing of a Mouse Neuronal Cell Line Using the PacBio Revio Sequencer

Manuel, J. G.·Heins, H. B.·Crocker, S.·Neidich, J. A.·Sadzewicz, L.·Tallon, L.·Turner, T. N.
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Abstract

Recently, Pacific Biosciences released a new highly accurate long-read sequencer called the Revio System that is projected to generate 30x HiFi whole-genome sequencing for the human genome within one sequencing SMRT Cell. Mouse and human genomes are similar in size. In this study, we sought to test this new sequencer by characterizing the genome and epigenome of the mouse neuronal cell line Neuro-2a. We generated long-read HiFi whole-genome sequencing on three Revio SMRT Cells, achieving a total coverage of 98x, with 30x, 32x, and 36x coverage respectively for each of the three Revio SMRT Cells. We performed several tests on these data including single-nucleotide variant and small insertion detection using GPU-accelerated DeepVariant, structural variant detection with pbsv, methylation detection with pb-CpG-tools, and generating de novo assemblies with the HiCanu and hifiasm assemblers. Overall, we find consistency across SMRT Cells in coverage, detection of variation, methylation, and de novo assemblies for each of the three SMRT Cells.

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Manuel, J. G., Heins, H. B., Crocker, S., Neidich, J. A., Sadzewicz, L., Tallon, L., Turner, T. N.. 2023-06-07. High Coverage Highly Accurate Long-Read Sequencing of a Mouse Neuronal Cell Line Using the PacBio Revio Sequencer. https://doi.org/10.1101/2023.06.06.543940

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