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

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

doi:10.1101/2020.07.23.218602

GenomicsbioRxivJul 23, 2020

Preprint

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

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

Abstract

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.

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