Nanopore Sequencing of the phi X 174 genome

Andrew H. Laszlo; Ian M. Derrington; Brian C. Ross; Henry Brinkerhoff; Andrew Adey; Ian C. Nova; Jonathan M. Craig; Kyle W. Langford; Jenny Mae Samson; Riza Daza; Kenji Doering; Jay Shendure; Jens H. Gundlach

arXiv · 1406.4214

Nanopore Sequencing of the phi X 174 genome

Andrew H. Laszlo·Ian M. Derrington·Brian C. Ross·Henry Brinkerhoff·Andrew Adey·Ian C. Nova·Jonathan M. Craig·Kyle W. Langford·Jenny Mae Samson·Riza Daza·Kenji Doering·Jay Shendure·Jens H. Gundlach

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Abstract

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. All methods and data are made fully available.

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Andrew H. Laszlo, Ian M. Derrington, Brian C. Ross, Henry Brinkerhoff, Andrew Adey, Ian C. Nova, Jonathan M. Craig, Kyle W. Langford, Jenny Mae Samson, Riza Daza, Kenji Doering, Jay Shendure, Jens H. Gundlach. 2014-06-18. Nanopore Sequencing of the phi X 174 genome. https://arxiv.org/abs/1406.4214

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