title: INC-Seq: accurate single molecule reads using nanopore sequencing.
abstract: Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing.
  
  
  
  We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA. Applying INC-Seq for 16S rRNA-based bacterial profiling generated full-length amplicon sequences with a median accuracy >97 %.
  
  
  
  INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore.|Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.
authors.forename: Chenhao
authors.initials: C
authors.lastname: Li
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Kern Rei
authors.initials: KR
authors.lastname: Chng
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Esther Jia Hui
authors.initials: EJ
authors.lastname: Boey
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Amanda Hui Qi
authors.initials: AH
authors.lastname: Ng
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilm
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Singapore. nagarajann@gis.a-star.edu.sg.|Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore. nagarajann@gis.a-star.edu.sg.
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058608:Nanopores; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Barcode sequencing; Consensus algorithms; Nanopore sequencing; Rolling circle amplification