title: Error analysis of idealized nanopore sequencing.
abstract: This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single-stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K-12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.
authors.affiliation: Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: O'Donnell
authors.forename: Hongyun
authors.initials: H
authors.lastname: Wang
authors.forename: William B
authors.initials: WB
authors.lastname: Dunbar
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006801:Humans; D008954:Models, Biological; D058608:Nanopores; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012815:Signal Processing, Computer-Assisted
chemical_list: D004277:DNA, Single-Stranded
keywords: DNA sequencing; Error rates; Nanopore; Nucleic acids; Single-molecule sequencing