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

By Franka J. Rang, Wigard P. Kloosterman, J. de Ridder. Genome Biology, 2018

557 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc34b829caa682bc02227f04807912c1d19a407f

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Citations in the corpus

Long-read human genome sequencing and its applications (2020, unknown): “ONT raw read accuracy is highly dependent on the base-calling algorithm used 38,57 , and recent improvements to these algorithms have increased raw read accuracy substantially in the past 5 years 38 .”
Nanopore sequencing technology, bioinformatics and applications (2021, methodology): “Overall, method development for base calling went through four stages 32,44,58,67,68 : (1) base calling from the segmented current data by HMM at the early stage and by recurrent neural network in late 2016, (2) base calling from raw current data in 2017, (3) using a flip–flop model for identifying…”
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar (2018, methodology): “utilization of different molecular approaches, including the 1D(2) method (where template and complementary strands of each fragment are sequenced) [40], tandem repeat consensus techniques [36, 51] or unique molecular identifiers [52].”
Sequencing DNA with nanopores: Troubles and biases (2021, background): “The task is made difficult by the rapid changeover of equipment, chemistry and programs [11].”