title: Decoding long nanopore sequencing reads of natural DNA.
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, which 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. This work provides a foundation for nanopore sequencing of long, natural DNA strands.
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Andrew H
authors: AH
authors: Laszlo
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Ian M
authors: IM
authors: Derrington
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Brian C
authors: BC
authors: Ross
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Henry
authors: 0000000327358048
authors: H
authors: Brinkerhoff
authors: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors: Andrew
authors: A
authors: Adey
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Ian C
authors: IC
authors: Nova
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Jonathan M
authors: JM
authors: Craig
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Kyle W
authors: KW
authors: Langford
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Jenny Mae
authors: JM
authors: Samson
authors: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors: Riza
authors: R
authors: Daza
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Kenji
authors: K
authors: Doering
authors: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors: Jay
authors: J
authors: Shendure
authors: Department of Physics, University of Washington, Seattle, Washington, USA.
authors: Jens H
authors: JH
authors: Gundlach
mesh_terms: D004247:DNA / Q000235:genetics*; D058608:Nanopores; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA