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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.

ABSTRACT: Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.

SUBMITTER: Rang FJ

PROVIDER: S-EPMC6045860 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.

Rang Franka J FJ Kloosterman Wigard P WP de Ridder Jeroen J

Genome biology 20180713 1

Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches d ...[more]

PMID: 30005597

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