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
… Here, we face the main computational challenges related to the analysis of nanopore data,
… for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically …

Fast nanopore sequencing data analysis with SLOW5

H Gamaarachchi, H Samarakoon, SP Jenner… - Nature …, 2022 - nature.com
… depends on the FAST5 file format, which does not allow efficient parallel analysisnanopore
data analysis. Using the example of DNA methylation profiling of a human genome, analysis

Poretools: a toolkit for analyzing nanopore sequence data

NJ Loman, AR Quinlan - Bioinformatics, 2014 - academic.oup.com
… community lacks a standardized toolkit for the analysis of nanopore datasets. … nanopore
sequencing devices from MinION™ for the purposes of quality control and downstream analysis. …

Improved data analysis for the MinION nanopore sequencer

M Jain, IT Fiddes, KH Miga, HE Olsen, B Paten… - Nature …, 2015 - nature.com
… read lengths make nanopores a promising technology for high-throughput sequencing.
We evaluated and optimized the performance of the MinION nanopore sequencer using M13 …

[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
… For example, genome 105 , transcriptome 42 and metagenome 106 assemblies have
shown superior performance with hybrid sequencing data compared to either error-prone long …

NanoPipe—a web server for nanopore MinION sequencing data analysis

V Shabardina, T Kischka, F Manske… - …, 2019 - academic.oup.com
… effortless and reliable analysis of MinION sequencing data for experienced bioinformaticians,
as … the basic algorithm necessary for MinION sequencing analysis from the first to last step. …

poRe: an R package for the visualization and analysis of nanopore sequencing data

M Watson, M Thomson, J Risse, R Talbot… - …, 2015 - academic.oup.com
… and visualize MinION nanopore sequencing data. As a package for R, poRe is available
for both Windows and Linux, and crucially the Windows version will allow data analysis on the …

[HTML][HTML] Computational methods for 16S metabarcoding studies using Nanopore sequencing data

A Santos, R van Aerle, L Barrientos… - Computational and …, 2020 - Elsevier
… can be trained with real sequencing data. The use of … of nanopore sequencing data and
limiting the impact of base modifications, insertions, and deletions commonly present in raw data

NanoR: A user-friendly R package to analyze and compare nanopore sequencing data

D Bolognini, N Bartalucci, A Mingrino, AM Vannucchi… - PloS one, 2019 - journals.plos.org
… (for sequencing kits 1D) or R9.5 (for sequencing kits 1D 2 ) nanopores arranged in 512
channels, is capable to generate 10–20 Gb of DNA sequence data over a 48 hours sequencing

NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles

RM Leggett, D Heavens, M Caccamo, MD Clark… - …, 2016 - academic.oup.com
… error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis
of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it …