Nanopore sequencing data analysis: state of the art, applications and challenges

A Magi, R Semeraro, A Mingrino, B Giusti… - Briefings in …, 2018 - academic.oup.com
… for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically
… of structural variants with an unprecedented accuracy and resolution. However, despite the …

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

D Senol Cali, JS Kim, S Ghose, C Alkan… - Briefings in …, 2019 - academic.oup.com
sequence analysis to understand their … , we analyze the tools associated with the multiple
steps in the genome assembly pipeline using nanopore sequence data in terms of accuracy, …

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

RA Bull, TN Adikari, JM Ferguson, JM Hammond… - Nature …, 2020 - nature.com
… due to common concerns around sequencing accuracy. To address this… in ONT sequencing
reads, highly accurate consensus-level … the capacity of nanopore sequencing to identify intra-…

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

FJ Rang, WP Kloosterman, J de Ridder - Genome biology, 2018 - Springer
… tools to process the MinION sequencing data and to improve accuracy have been developed,
tested… approaches to improve the accuracy of nanopore sequencing data by focusing on (i) …

Accurate data process for nanopore analysis

Z Gu, YL Ying, C Cao, P He, YT Long - Analytical chemistry, 2015 - ACS Publications
… Here, we propose an automatic and accurate nanopore data process that includes … accurately
measure the dwell time. We demonstrated that the DBC method improves the accuracy of …

Species-specific basecallers improve actual accuracy of nanopore sequencing in plants

S Ferguson, T McLay, RL Andrew, JJ Bruhl… - Plant Methods, 2022 - Springer
… truth dataset for model training and basecaller accuracy analysis. By removing short (1 Kbp)
… genome is not used during basecaller training or accuracy analysis we don’t report on its …

Performance of neural network basecalling tools for Oxford Nanopore sequencing

RR Wick, LM Judd, KE Holt - Genome biology, 2019 - Springer
… Basecalling accuracy can be assessed at the read level (read accuracy) or in terms … accuracy
of the consensus sequence (consensus accuracy). Read accuracy measures the sequence

Efficient assembly of nanopore reads via highly accurate and intact error correction

Y Chen, F Nie, SQ Xie, YF Zheng, Q Dai, T Bray… - Nature …, 2021 - nature.com
… Next, we analyzed sequencing errors in each nanopore read. We first aligned each read
onto the reference genomes. We partitioned each read into 500-bp long subsequences and …

Accurate expression quantification from nanopore direct RNA sequencing with NanoCount

J Gleeson, A Leger, YDJ Prawer, TA Lane… - Nucleic acids …, 2022 - academic.oup.com
… of short and long-read sequencing methods that require RNA … We developed NanoCount
for fast, accurate transcript … cells, we show that DRS accurately quantifies RNA expression and …

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing

W Liu-Wei, W van der Toorn, P Bohn, M Hölzer… - BMC genomics, 2024 - Springer
… We present the first comprehensive evaluation of sequencing accuracy and characterisation
… that for sequencing kits SQK-RNA001 and SQK-RNA002, the median read accuracy ranged …