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Foox J , Tighe SW , Nicolet CM , Zook JM , Byrska-Bishop M , Clarke WE , Khayat MM , Mahmoud M , Laaguiby PK , Herbert ZT , Warner D , Grills GS , Jen J , Levy S , Xiang J , Alonso A , Zhao X , Zhang W , Teng F , Zhao Y , Lu H , Schroth GP , Narzisi G , Farmerie W , Sedlazeck FJ , Baldwin DA , Mason CE
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
Nat Biotechnol. 2021 Sep;39(9) :1129-1140
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Abstract
Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.
Notes
1546-1696 Foox, Jonathan Tighe, Scott W Orcid: 0000-0002-3988-0741 Nicolet, Charles M Zook, Justin M Orcid: 0000-0003-2309-8402 Byrska-Bishop, Marta Orcid: 0000-0002-9118-1032 Clarke, Wayne E Khayat, Michael M Orcid: 0000-0001-5452-3147 Mahmoud, Medhat Orcid: 0000-0002-2553-4231 Laaguiby, Phoebe K Herbert, Zachary T Orcid: 0000-0001-9401-2464 Warner, Derek Grills, George S Jen, Jin Levy, Shawn Orcid: 0000-0002-1369-5740 Xiang, Jenny Alonso, Alicia Zhao, Xia Zhang, Wenwei Teng, Fei Orcid: 0000-0003-4913-7094 Zhao, Yonggang Lu, Haorong Orcid: 0000-0003-0132-8166 Schroth, Gary P Orcid: 0000-0002-3055-056x Narzisi, Giuseppe Orcid: 0000-0003-1118-8849 Farmerie, William Orcid: 0000-0002-1627-8774 Sedlazeck, Fritz J Orcid: 0000-0001-6040-2691 Baldwin, Don A Orcid: 0000-0002-1853-9253 Mason, Christopher E Orcid: 0000-0002-1850-1642 R25 EB020393/EB/NIBIB NIH HHS/United States R01 NS076465/NS/NINDS NIH HHS/United States R01 AI125416/AI/NIAID NIH HHS/United States R01 ES021006/ES/NIEHS NIH HHS/United States R21 AI129851/AI/NIAID NIH HHS/United States R01 MH117406/MH/NIMH NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Validation Study United States Nat Biotechnol. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5. Epub 2021 Sep 9.