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Improved data analysis for the MinION nanopore sequencer

Tool

Date: 6th January 2015 | Source:

Authors: Miten Jain Ian T Fiddes Karen H Miga Hugh E Olsen Benedict Paten Mark Akeson

Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing. We evaluated and optimised the performance of the MinION nanopore sequencer using M13 genomic DNA and used expectation maximisation 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 marginalisation 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.

Nature - Methods

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