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

TitlePerformance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.
Publication TypeJournal Article
Year of Publication2021
AuthorsFoox, 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
JournalNat Biotechnol
Date Published2021 Sep
KeywordsBase Pair Mismatch, Benchmarking, DNA, DNA, Bacterial, Genome, Bacterial, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA

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.

Alternate JournalNat Biotechnol
PubMed ID34504351
PubMed Central IDPMC8985210
Grant ListR01 AI125416 / AI / NIAID NIH HHS / United States
R01 ES021006 / ES / NIEHS NIH HHS / United States
R21 AI129851 / AI / NIAID NIH HHS / United States
U01 DA053941 / DA / NIDA NIH HHS / United States
R01 MH117406 / MH / NIMH NIH HHS / United States
R25 EB020393 / EB / NIBIB NIH HHS / United States
R01 AI151059 / AI / NIAID NIH HHS / United States
R01 NS076465 / NS / NINDS NIH HHS / United States
UM1 HG008898 / HG / NHGRI NIH HHS / United States