INC-Seq: accurate single molecule reads using nanopore sequencing

Abstract

BackgroundNanopore 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.ResultsWe 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 %.ConclusionsINC-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-016-0140-7) contains supplementary material, which is available to authorized users.

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“…At the time of writing, MinION sequencing (R9 pore chemistry) has raw high quality (so called '2D reads') read error rates of around 5% (J. Quick, personal communication), which compares unfavourably with the error rates of other technologies (Illumina (<0.1%), Ion Torrent (~1%), but not PacBio (13% single pass)) 132 , although accuracy can been improved using circular consensus read sequencing 133,134 .…”

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