title: Analysis of nanopore data using hidden Markov models.
abstract: BACKGROUND
  Nanopore-based sequencing techniques can reconstruct properties of biosequences by analyzing the sequence-dependent ionic current steps produced as biomolecules pass through a pore. Typically this involves alignment of new data to a reference, where both reference construction and alignment have been performed by hand.
  
  
  RESULTS
  We propose an automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be simply incorporated into the model. Previously, the M2MspA nanopore was shown to be sensitive enough to distinguish between cytosine, methylcytosine and hydroxymethylcytosine. We validated our automated methodology on a subset of that data by automatically calculating an error rate for the distinction between the three cytosine variants and show that the automated methodology produces a 2-3% error rate, lower than the 10% error rate from previous manual segmentation and alignment.
  
  
  METHODS
  The data, output, scripts and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/Data/tree/master/Automation.
authors: Nanopore Group, Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA.
authors: Jacob
authors: J
authors: Schreiber
authors: Nanopore Group, Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA.
authors: Kevin
authors: K
authors: Karplus
mesh_terms: D044503:5-Methylcytosine / Q000737:chemistry / Q000031:analogs & derivatives; D000465:Algorithms; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry; D019175:DNA Methylation; D057890:Epigenomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008390:Markov Chains; D058608:Nanopores; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
references: J Mol Biol. 2001 Jan 19;305(3):567-80
references: 11152613
references: PLoS One. 2011;6(10):e25723
references: 21991340
references: Nucleic Acids Res. 1998 Jan 1;26(1):320-2
references: 9399864
references: Bioinformatics. 1998;14(9):755-63
references: 9918945
references: BMC Bioinformatics. 2007;8 Suppl 7:S12
references: 18047711
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W492-7
references: 19483096
references: Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18910-5
references: 24167260
references: Science. 2011 Sep 2;333(6047):1300-3
references: 21778364
references: Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3
references: 8943010
references: Nat Biotechnol. 2012 Apr;30(4):344-8
references: 22334048
references: Biophys J. 2012 May 16;102(10):L37-9
references: 22677395
references: Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18904-9
references: 24167255
references: J Am Chem Soc. 2010 Dec 22;132(50):17961-72
references: 21121604