Improved data analysis for the MinION nanopore sequencer

Improved data analysis for the MinION nanopore sequencer. Jain, M., Fiddes, I., T., Miga, K., H., Olsen, H., E., Paten, B., & Akeson, M. Nature Methods, 12(4):351-356, 2015.

Paper

Improved data analysis for the MinION nanopore sequencer [link]

Website abstract bibtex

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.

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 year = {2015},
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 pages = {351-356},
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 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.},
 bibtype = {article},
 author = {Jain, Miten and Fiddes, Ian T and Miga, Karen H and Olsen, Hugh E and Paten, Benedict and Akeson, Mark},
 journal = {Nature Methods},
 number = {4}
}

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