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Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

By Jonathan Foox, Scott W Tighe, Charles M Nicolet, Justin M Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M Khayat, Medhat Mahmoud, Phoebe K Laaguiby, Zachary T Herbert, Derek Warner, George S Grills, Jin Jen, Shawn E. Levy, Jenny Xiang, Alicia Alonso, Gary P Schroth, Fritz J. Sedlazeck, Giuseppe Narzisi, William Farmerie, Don A Baldwin, Christopher E Mason

Posted 24 Jul 2020
bioRxiv DOI: 10.1101/2020.07.23.218602

Massively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Phase II Study to measure quality and reproducibility of DNA sequencing. Replicates of human and bacterial reference DNA samples were generated across multiple sequencing platforms, including well-established technologies such as Illumina, ThermoFisher Ion Torrent, and Pacific Biosciences, as well as emerging technologies such as BGI, Genapsys, and Oxford Nanopore. A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection of small-scale polymorphisms and large-scale structural variants. This study provides a comprehensive baseline resource for continual benchmarking as chemistries, methods, and platforms evolve for DNA sequencing. ### Competing Interest Statement G.P.S is employed by Illumina Inc. All other authors declare no competing financial interests.

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