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INC-Seq: accurate single molecule reads using nanopore sequencing.

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.

SUBMITTER: Li C

PROVIDER: S-EPMC4970289 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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INC-Seq: accurate single molecule reads using nanopore sequencing.

Li Chenhao C Chng Kern Rei KR Boey Esther Jia Hui EJ Ng Amanda Hui Qi AH Wilm Andreas A Nagarajan Niranjan N

GigaScience 20160802 1

<h4>Background</h4>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.<h4>Results</h4>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 ...[more]

PMID: 27485345

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