Improved data analysis for the MinION nanopore sequencer

By Miten Jain, Ian T. Fiddes, Karen H. Miga, Hugh E. Olsen, Benedict Paten, Mark Akeson. Nature Methods, 2015

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Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing. We evaluated and optimized the performance of the MinION nanopore sequencer using M13 genomic DNA and used expectation maximization to obtain robust maximum-likelihood estimates for insertion, deletion and substitution error rates (4.9%, 7.8% and 5.1%, respectively). Over 99% of high-quality 2D MinION reads mapped to the reference at a mean identity of 85%. We present a single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By pairing our high-confidence alignment strategy with long MinION reads, we resolved the copy number for a cancer-testis gene family (CT47) within an unresolved region of human chromosome Xq24.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5647e4a5733f254cd7531af5bc4293bc8f59c5f7

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Citations in the corpus

Advances and Trends in Omics Technology Development (2022, background): “TGS, the third revolution in sequencing technology as enabled by Paciﬁc Biosciences (PacBio, 2011) (76) and Oxford Nanopore Technologies (ONT, 2014) (77), is a single molecular and real-time sequencing technique that allows for the long-read sequencing with low alignment and mapping errors during…”
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