Assessing the performance of the Oxford Nanopore Technologies MinION

By T. Laver, James W. Harrison, P. O'Neill, K. Moore, A. Farbos, Konrad H. Paszkiewicz, David J. Studholme. Biomolecular Detection and Quantification, 2015

521 citations recorded by the source corpus.

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7fb0bbffdb5031e7867a4948a8f315719fb1617d

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Citations in the corpus

Computational pan-genomics: status, promises and challenges (2016, methodology): “The MinION device (Oxford Nanopore Technologies) [118] provides even longer reads of single DNA molecules, but has been reported to exhibit GC biases [71].”
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing (2017, unknown): “For DNA this function has been resolved with considerable accuracy by Oxford Nanopore technologies, but significant errors remain in the 1D base calls (between 70%-90% accuracy reported though this depends strongly on the version of pore used 20, 21, 36 ).”
MinION Analysis and Reference Consortium: Phase 1 data release and analysis (2015, unknown): “…early 2015 (Ammar et al ., 2015; Ashton et al. , 2015; Greninger et al ., 2015; Jain et al., 2015; Karlsson et al ., 2015; Kilianski et al ., 2015; Laver et al ., 2015; Loman et al ., 2015; Mulley & Hargreaves, 2015; Quick et al ., 2014; Urban et al., 2015; Wang et al. , 2015) and these provided…”
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy (2018, methodology): “When the MinION was first introduced, reads showed an accuracy of less than 60% [9, 10].”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “To simplify this task, PATRIC integrates the Assembly RAST (ARAST) service to enable researchers to assemble short reads that are single or paired-end (typically from Illumina), and also long reads that include bax.h5 read files and filtered FASTQ files from PacBio (9) and Oxford Nanopore (10,11).”
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms (2019, background): “Recently, with the development of sequencing technologies, especially rapid advances in third generation sequencing including Pacific Biosciences (Eid et al. 2009) and Oxford Nanopore Technologies (Laver et al. 2015), BioNano genome mapping (Cao et al. 2014) and High-46 throughput chromatin conforma”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “The read length proﬁle of the ONT data is very similar to that of PacBio, with a maximum length up to a few hundred thousand base pairs [11,12].”
PacBio Sequencing and Its Applications (2015, background): “Although only very limited studies and data of ONT have been published, it shows similar advantages and disadvantages: ONT reads are long but are of even higher error rate than PacBio sequencing [22].”
Third generation sequencing: technology and its potential impact on evolutionary biodiversity research (2016, background): “The output of the published studies ranged from 90 to 490 mbp per 48 hours, with average read lengths around 6 kbp and maximum read lengths of up to 150 kbp (Ashton et al., 2015; Goodwin et al., in press; Laver et al., 2015; Quick, Quinlan, & Loman, 2014).”
Sequencing DNA with nanopores: Troubles and biases (2021, result): “This was already noted in [31], although quality scores are now much closer to Phred scores than they were then.”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, methodology): “[87] have assessed the performance of an earlier version of the MinION sequencing device and concluded that “the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhan”
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis (2018, background): “By sequencing single molecules, they can also avoid the need for PCR amplification, hence reducing coverage biases [207,208].”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “While it can generate reads as long as 98 kB, it is again plagued by extremely high error rates (Laver et al. 2015).”