June 1, 2021

Near perfect de novo assemblies of eukaryotic genomes using PacBio long read sequencing.

Author(s): Schatz, M.C. and Deshpande, P. and Gurtowski, J. and Eskipehlivan, S.M. and Kramer, M. and Lee, H. and Goodwin, S. and Antoniou, E. and Heiner, C. and Khitrov, G. and McCombie, W. R.

Third generation single molecule sequencing technology from Pacific Biosciences, Moleculo, Oxford Nanopore, and other companies are revolutionizing genomics by enabling the sequencing of long, individual molecules of DNA and RNA. One major advantage of these technologies over current short read sequencing is the ability to sequence much longer molecules, thousands or tens of thousands of nucleotides instead of mere hundreds. This capacity gives researchers substantially greater power to probe into microbial, plant, and animal genomes, but it remains unknown on how to best use these data. To answer this, we systematically evaluated the human genome and 25 other important genomes across the tree of life ranging in size from 1Mbp to 3Gbp in an attempt to answer how long the reads need to be and how much coverage is necessary to completely assemble their chromosomes with single molecule sequencing. We also present a novel error correction and assembly algorithm using a combination of PacBio and pre-assembled Illumina sequencing. This new algorithm greatly outperforms other published hybrid algorithms.

Organization: Cold Spring Harbor Laboratory
Year: 2014

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