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bioRxiv · 10.1101/038042

INC-Seq: Accurate single molecule reads using nanopore sequencing

Chenhao Li·Kern Rei Chng·Jia Hui Esther Boey·Hui Qi Amanda Ng·Andreas Wilm·Niranjan Nagarajan
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Abstract

Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. Several applications, including RNA-seq, haplotype sequencing and 16S sequencing, are however limited by its relatively high single read error rate (>10%). We present INC-Seq (Intramolecular-ligated Nanopore Consensus Sequencing) 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 median accuracy >97%. INC-Seq reads enable 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.

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Chenhao Li, Kern Rei Chng, Jia Hui Esther Boey, Hui Qi Amanda Ng, Andreas Wilm, Niranjan Nagarajan. 2016-01-27. INC-Seq: Accurate single molecule reads using nanopore sequencing. https://doi.org/10.1101/038042

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