title: Improved data analysis for the MinION nanopore sequencer.
abstract: 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.
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Miten
authors: M
authors: Jain
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Ian T
authors: IT
authors: Fiddes
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Karen H
authors: KH
authors: Miga
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Hugh E
authors: HE
authors: Olsen
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Benedict
authors: B
authors: Paten
authors: 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
authors: Mark
authors: M
authors: Akeson
mesh_terms: D000465:Algorithms; D018628:Gene Dosage; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058608:Nanopores; D009369:Neoplasms / Q000235:genetics