Beyond assembly: the increasing flexibility of single-molecule sequencing technology

PW Hook, W Timp - Nature Reviews Genetics, 2023 - nature.com
The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

Portable nanopore-sequencing technology: Trends in development and applications

P Chen, Z Sun, J Wang, X Liu, Y Bai, J Chen… - Frontiers in …, 2023 - frontiersin.org
Sequencing technology is the most commonly used technology in molecular biology
research and an essential pillar for the development and applications of molecular biology …

Simulation of nanopore sequencing signal data with tunable parameters

H Gamaarachchi, JM Ferguson… - Genome …, 2024 - genome.cshlp.org
In silico simulation of high-throughput sequencing data is a technique used widely in the
genomics field. However, there is currently a lack of effective tools for creating simulated …

Efficient real-time selective genome sequencing on resource-constrained devices

PJ Shih, H Saadat, S Parameswaran… - …, 2023 - academic.oup.com
Background Third-generation nanopore sequencers offer selective sequencing or “Read
Until” that allows genomic reads to be analyzed in real time and abandoned halfway if not …

Real‐time genomics for One Health

L Urban, A Perlas, O Francino… - Molecular Systems …, 2023 - embopress.org
The ongoing degradation of natural systems and other environmental changes has put our
society at a crossroad with respect to our future relationship with our planet. While the …

Accelerated nanopore basecalling with SLOW5 data format

H Samarakoon, JM Ferguson, H Gamaarachchi… - …, 2023 - academic.oup.com
Motivation Nanopore sequencing is emerging as a key pillar in the genomic technology
landscape but computational constraints limiting its scalability remain to be overcome. The …

Accelerated dynamic time war** on GPU for selective nanopore sequencing

H Sadasivan, D Stiffler, A Tirumala, J Israeli… - bioRxiv, 2023 - biorxiv.org
The design and supply of RT-PCR primers for accurate virus testing is a complex process.
The MinION is a revolutionary portable nanopore DNA sequencer that may be used to …

DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing

A Senanayake, H Gamaarachchi, D Herath, R Ragel - BMC bioinformatics, 2023 - Springer
Background Nanopore sequencing allows selective sequencing, the ability to
programmatically reject unwanted reads in a sample. Selective sequencing has many …

[HTML][HTML] Rapid real-time squiggle classification for read until using rawmap

H Sadasivan, J Wadden, K Goliya… - Archives of clinical …, 2023 - ncbi.nlm.nih.gov
Abstract ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively
sequence reads of target species in real-time. This enables efficient microbial enrichment for …

The application of metagenomics to study microbial communities and develop desirable traits in fermented foods

M Srinivas, O O'Sullivan, PD Cotter, D Sinderen… - Foods, 2022 - mdpi.com
The microbial communities present within fermented foods are diverse and dynamic,
producing a variety of metabolites responsible for the fermentation processes, imparting …