MinION Analysis and Reference Consortium: Phase 1 data release and analysis

By C. Ip, M. Loose, John R. Tyson, M. Cesare, B. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, V. Zalunin, John M. Urban and 15 more. F1000Research, 2015

302 citations recorded by the source corpus.

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.

Subfields: Biomedical Engineering, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2035fccfda5c19c1930f556863fe0b03854daa9e

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Citations in the corpus

WhatsHap: fast and accurate read-based phasing (2016, background): “2 Tools Driven by the advances in third-generation sequencing [16, 17, 18] and the corresponding growth in read length, read-based phasing has been gaining considerable attention [19].”
Three decades of nanopore sequencing (2016, result): “In a recent study published online 36 , an international consortium of five laboratories associated with MAP compared results from the same strain of E. coli K-12, using identical protocols for extraction, shearing and library preparations.”
Sequencing DNA with nanopores: Troubles and biases (2021, methodology): “In the Phase 1 early access program from Nanopore, a study from the MinION Analysis and Reference Consortium [3] showed that the 2D pass reads had a total error of 10.5%, including about 3% for mismatch and insertion and slightly more for deletion.”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “The 20 (cid:4) MinION reads are a subset of 48 (cid:4) reads from [13], while the 20 (cid:4) PacBio reads were selected from a set of 25 (cid:4) E . coli K12 MG1655 reads downloaded from http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR.”
Generations of Sequencing Technologies: From First to Next Generation (2017, background): “However, MinION produces a high error rate of ~12% distributed about ~3% mismatchs, ~4% insertions and ~5% deletions [53].”
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy (2018, background): “Based on data from 1 [9]; 2 [10]; 3 [50]; 4 [51]; 5 [33]; 6 [28]; 7 [52]; 8 [53];”