Journal Article

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

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

2021

Overview

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. Next-generation sequencing platforms are benchmarked using human, bacterial and metagenomics reference materials.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/1647/48 / 631/208/514/2254 / 631/61/212 / 631/61/514/1948 / Agriculture / Analysis / Base Pair Mismatch / Benchmarking / Benchmarks / Bioinformatics / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Deoxyribonucleic acid / Design of experiments / DNA / DNA - genetics / DNA sequencing / DNA, Bacterial - genetics / Experimental design / Forecasts and trends / Gene mapping / Genetic testing / Genome, Bacterial / Genome, Human / High-Throughput Nucleotide Sequencing - methods / High-Throughput Nucleotide Sequencing - standards / Humans / Insertion / Life Sciences / Mapping / Metagenomics / Methods / Next-generation sequencing / Nucleotide sequencing / Performance assessment / Performance-based assessment / Platforms / Reference materials / Sequence Analysis, DNA - methods / Sequence Analysis, DNA - standards