Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

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 Levy; Jenny Xiang; Alicia Alonso; Xia Zhao; Wenwei Zhang; Fei Teng; Yonggang Zhao; Haorong Lu; Gary P. Schroth; Giuseppe Narzisi; William Farmerie; Fritz J. Sedlazeck; Don A. Baldwin; Christopher E. Mason

doi:10.1038/s41587-021-01049-5

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

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 Levy, Jenny Xiang, Alicia Alonso, Xia Zhao, Wenwei Zhang, Fei Teng, Yonggang ZhaoHaorong Lu, Gary P. Schroth, Giuseppe Narzisi, William Farmerie, Fritz J. Sedlazeck, Don A. Baldwin, Christopher E. Mason

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66 Scopus citations

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.

Original language	English
Pages (from-to)	1129-1140
Number of pages	12
Journal	Nature Biotechnology
Volume	39
Issue number	9
DOIs	https://doi.org/10.1038/s41587-021-01049-5
State	Published - Sep 2021

Keywords

Base Pair Mismatch
Benchmarking
DNA, Bacterial/genetics
DNA/genetics
Genome, Bacterial
Genome, Human
High-Throughput Nucleotide Sequencing/methods
Humans
Sequence Analysis, DNA/methods

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10.1038/s41587-021-01049-5

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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., Jen, J., Levy, S., Xiang, J., Alonso, A., Zhao, X., Zhang, W., Teng, F., ... Mason, C. E. (2021). Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nature Biotechnology, 39(9), 1129-1140. https://doi.org/10.1038/s41587-021-01049-5

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title = "Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study",

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.",

keywords = "Base Pair Mismatch, Benchmarking, DNA, Bacterial/genetics, DNA/genetics, Genome, Bacterial, Genome, Human, High-Throughput Nucleotide Sequencing/methods, Humans, Sequence Analysis, DNA/methods",

author = "Jonathan Foox and Tighe, {Scott W.} and Nicolet, {Charles M.} and Zook, {Justin M.} and Marta Byrska-Bishop and Clarke, {Wayne E.} and Khayat, {Michael M.} and Medhat Mahmoud and Laaguiby, {Phoebe K.} and Herbert, {Zachary T.} and Derek Warner and Grills, {George S.} and Jin Jen and Shawn Levy and Jenny Xiang and Alicia Alonso and Xia Zhao and Wenwei Zhang and Fei Teng and Yonggang Zhao and Haorong Lu and Schroth, {Gary P.} and Giuseppe Narzisi and William Farmerie and Sedlazeck, {Fritz J.} and Baldwin, {Don A.} and Mason, {Christopher E.}",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2021",

month = sep,

doi = "10.1038/s41587-021-01049-5",

language = "English",

volume = "39",

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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 2021, 'Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study', Nature Biotechnology, vol. 39, no. 9, pp. 1129-1140. https://doi.org/10.1038/s41587-021-01049-5

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AU - Foox, Jonathan

AU - Tighe, Scott W.

AU - Nicolet, Charles M.

AU - Zook, Justin M.

AU - Byrska-Bishop, Marta

AU - Clarke, Wayne E.

AU - Khayat, Michael M.

AU - Mahmoud, Medhat

AU - Laaguiby, Phoebe K.

AU - Herbert, Zachary T.

AU - Warner, Derek

AU - Grills, George S.

AU - Jen, Jin

AU - Levy, Shawn

AU - Xiang, Jenny

AU - Alonso, Alicia

AU - Zhao, Xia

AU - Zhang, Wenwei

AU - Teng, Fei

AU - Zhao, Yonggang

AU - Lu, Haorong

AU - Schroth, Gary P.

AU - Narzisi, Giuseppe

AU - Farmerie, William

AU - Sedlazeck, Fritz J.

AU - Baldwin, Don A.

AU - Mason, Christopher E.

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AB - 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.

KW - Base Pair Mismatch

KW - Benchmarking

KW - DNA, Bacterial/genetics

KW - DNA/genetics

KW - Genome, Bacterial

KW - Genome, Human

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Sequence Analysis, DNA/methods

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SP - 1129

EP - 1140

JO - Nature Biotechnology

JF - Nature Biotechnology

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ER -

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

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Keywords

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