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

Foox, J.; Tighe, S. W.; Nicolet, C. M.; Zook, J. M.; Byrska-Bishop, M.; Clarke, W. E.; Khayat, M. M.; Mahmoud, M.; Laaguiby, P. K.; Herbert, Z. T.; Warner, D.; Grills, G. S.; Levy, S.; Schroth, G. P.; Sedlazeck, F. J.; Narzisi, G.; Farmerie, W.; Baldwin, D. A.; Mason, C. E.; Mason, C.

doi:10.1101/2020.07.23.218602

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bioRxiv · 10.1101/2020.07.23.218602

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

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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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Foox, J., Tighe, S. W., Nicolet, C. M., Zook, J. M., Byrska-Bishop, M., Clarke, W. E., Khayat, M. M., Mahmoud, M., Laaguiby, P. K., Herbert, Z. T., Warner, D., Grills, G. S., Levy, S., Schroth, G. P., Sedlazeck, F. J., Narzisi, G., Farmerie, W., Baldwin, D. A., Mason, C. E., Mason, C.. 2020-07-24. Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study. https://doi.org/10.1101/2020.07.23.218602

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