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Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

Journal Article · · Scientific Reports
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  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
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Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.
Research Organization:
Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA)
Grant/Contract Number:
AC04-94AL85000
OSTI ID:
1430904
Report Number(s):
SAND--2018-0811J; 661556
Journal Information:
Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 8; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.) journal June 2019
Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria journal August 2019
Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion text January 2019
Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage journal April 2019
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm journal April 2020
Long reads: their purpose and place journal May 2018
Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing journal March 2020
Long reads: their purpose and place. text January 2018
Long-Read Sequencing Emerging in Medical Genetics journal May 2019
Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion journal October 2019

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