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
Nanopore sequencing technology has the potential to render other sequencing
technologies obsolete with its ability to generate long reads and provide portability …

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
The nanopore sequencing process is based on the transit of a DNA molecule through a
nanoscopic pore, and since the 90s is considered as one of the most promising approaches …

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

FJ Rang, WP Kloosterman, J de Ridder - Genome biology, 2018 - Springer
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 …

De novo sequencing and variant calling with nanopores using PoreSeq

T Szalay, JA Golovchenko - Nature biotechnology, 2015 - nature.com
The accuracy of sequencing single DNA molecules with nanopores is continually improving,
but de novo genome sequencing and assembly using only nanopore data remain …

Poretools: a toolkit for analyzing nanopore sequence data

NJ Loman, AR Quinlan - Bioinformatics, 2014 - academic.oup.com
Motivation: Nanopore sequencing may be the next disruptive technology in genomics, owing
to its ability to detect single DNA molecules without prior amplification, lack of reliance on …

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

S Goodwin, J Gurtowski, S Ethe-Sayers… - Genome …, 2015 - genome.cshlp.org
Monitoring the progress of DNA molecules through a membrane pore has been postulated
as a method for sequencing DNA for several decades. Recently, a nanopore-based …

Oxford Nanopore MinION sequencing and genome assembly

H Lu, F Giordano, Z Ning - Genomics, Proteomics and …, 2016 - academic.oup.com
The revolution of genome sequencing is continuing after the successful second-generation
sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by …

Genome assembly using Nanopore-guided long and error-free DNA reads

MA Madoui, S Engelen, C Cruaud, C Belser, L Bertrand… - BMC genomics, 2015 - Springer
Background Long-read sequencing technologies were launched a few years ago, and in
contrast with short-read sequencing technologies, they offered a promise of solving …

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

MD Cao, SH Nguyen, D Ganesamoorthy… - Nature …, 2017 - nature.com
Third generation sequencing technologies provide the opportunity to improve genome
assemblies by generating long reads spanning most repeat sequences. However, current …

Nanopore sequencing: Review of potential applications in functional genomics

N Kono, K Arakawa - Development, growth & differentiation, 2019 - Wiley Online Library
Molecular biology has been led by various measurement technologies, and increased
throughput has developed omics analysis. The development of massively parallel …