INC-Seq: accurate single molecule reads using nanopore sequencing. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Li, Chenhao; Chng, Kern; Boey, Esther; Ng, Amanda; Wilm, Andreas; Nagarajan, Niranjan
• Is Part Of: GigaScience. Volume 5:Issue 1(2016)
• Page Start: 1
• Page End: 11
• Publication Date: 2016-12
• Subjects: Nanopore sequencing -- Rolling circle amplification -- Barcode sequencing -- Consensus algorithms; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1186/s13742-016-0140-7
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract Background 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. Results 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 %. Conclusions 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.