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

Published

September 9, 2021

Author(s)

Justin Zook, Jonathan Foox, Christopher E. Mason

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.

Citation

Nature Biotechnology

Volume

39

Pub Type

Journals

Download Paper

Local Download

Keywords

genomics, DNA sequencing, interlaboratory study, Next Generation Sequencing

Citation

Zook, J. , Foox, J. and Mason, C. (2021), Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study, Nature Biotechnology, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=927948 (Accessed October 10, 2025)