A first look at the Oxford Nanopore MinION sequencer
Top Cited Papers
- 24 September 2014
- journal article
- research article
- Published by Wiley in Molecular Ecology Resources
- Vol. 14 (6), 1097-1102
- https://doi.org/10.1111/1755-0998.12324
Abstract
Oxford Nanopore's third-generation single-molecule sequencing platform promises to decrease costs for reagents and instrumentation. After a 2-year hiatus following the initial announcement, the first devices have been released as part of an early access program. We explore the performance of this platform by resequencing the lambda phage genome, and amplicons from a snake venom gland transcriptome. Although the handheld MinION sequencer can generate more than 150 megabases of raw data in one run, at most a quarter of the resulting reads map to the reference, with less than average 10% identity. Much of the sequence consists of insertion/deletion errors, or is seemingly without similarity to the template. Using the lambda phage data as an example, although the reads are long, averaging 5 kb, at best 890 ± 1932 bases per mapped read could be matched to the reference without soft clipping. In the course of a 36 h run on the MinION, it was possible to resequence the 48 kb lambda phage reference at 16× coverage. Currently, substantially larger projects would not be feasible using the MinION. Without increases in accuracy, which would be required for applications such as genome scaffolding and phasing, the current utility of the MinION appears limited. Library preparation requires access to a molecular laboratory, and is of similar complexity and cost to that of other next-generation sequencing platforms. The MinION is an exciting step in a new direction for single-molecule sequencing, though it will require dramatic decreases in error rates before it lives up to its promise.Keywords
Funding Information
- Okinawa Institute of Science and Technology
This publication has 26 references indexed in Scilit:
- DNA Base-Calling from a Nanopore Using a Viterbi AlgorithmBiophysical Journal, 2012
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011
- Field guide to next‐generation DNA sequencersMolecular Ecology Resources, 2011
- Sequence-specific error profile of Illumina sequencersNucleic Acids Research, 2011
- Haplotype-resolved genome sequencing of a Gujarati Indian individualNature Biotechnology, 2011
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataGenome Research, 2010
- A flexible and efficient template format for circular consensus sequencing and SNP detectionNucleic Acids Research, 2010
- Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encodingGenome Research, 2009
- Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanoporeProceedings of the National Academy of Sciences of the United States of America, 2009
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008