Results 81 to 90 of about 29,607 (257)

De novo Nanopore read quality improvement using deep learning

BMC Bioinformatics, 2019
Background Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification.
Nathan LaPierre, Rob Egan, Wei Wang, Zhong Wang   +3 more
doaj   +1 more source

Human genome sequencing on Oxford Nanopore PromethION

, 2018
For benchmarking, development and evaluation of tools we have sequenced the Yoruban reference genome NA19240 to 80x coverage using Oxford Nanopore PromethION. Additionally, we are developing a workflow for efficient detection and annotation of structural variation from long read sequencing data, integrating tools such as Sniffles and NanoSV.
Coster, Wouter De, Pooter, Tim De, Roeck, Arne De, D'Hert, Svenn, Dongen, Jasper Van, Rijk, Peter De, Strazisar, Mojca, Broeckhoven, Christine Van   +7 more
openaire   +1 more source

A cost‐effective DNA extraction protocol for long‐read sequencing in non‐model plants

Applications in Plant Sciences, EarlyView.
Abstract Premise Third‐generation sequencing has revolutionized genomics, enabling in‐depth analysis of genome sequence, structure, and epigenetic features. Yet, extracting high‐quality DNA for long‐read sequencing remains a bottleneck—particularly in non‐model plants, such as mature trees growing in natural environments, which often contain abundant ...
Sofia Gaischuk, Cintia F. Marchetti, Ezequiel Petrillo, Fernando A. Rabanal, Detlef Weigel, Nicolás Bellora, M. Verónica Arana   +6 more
wiley   +1 more source

A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology

mSystems
Whole-genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen.
Andrea M. Schiffer, Arafat Rahman, Wendy Sutton, Melodie L. Putnam, Alexandra J. Weisberg   +4 more
doaj   +1 more source

Forensic DNA phenotyping using Oxford Nanopore Sequencing system

ELECTROPHORESIS
AbstractIn forensic science, the demand for precision, consistency, and cost‐effectiveness has driven the exploration of next‐generation sequencing technologies. This study investigates the potential of Oxford Nanopore Sequencing (ONT) Technology for analyzing the HIrisPlex‐S panel, a set of 41 single nucleotide polymorphism (SNP) markers used to ...
Veysel Sapan, Sumeyye Zulal Simsek, Gonul Filoğlu, Ozlem Bulbul   +3 more
openaire   +3 more sources

Molecular methods for differentiating Phragmites australis subspecies and identification of hybrid stands in the Upper Midwestern United States

Applications in Plant Sciences, EarlyView.
Abstract Premise In North America, Phragmites australis (common reed) has drawn a great deal of research attention. Non‐native P. australis subsp. australis is a noxious weed that has locally displaced native P. australis subsp. americanus in some areas.
Nicholas P. Tippery, Daniel J. Larkin, Julia Bohnen, Douglas L. Wendell, Neil O. Anderson, Susan M. Galatowitsch, Marie Abbey, Alan G. Smith, Andrzej K. Noyszewski   +8 more
wiley   +1 more source

Is Oxford Nanopore Technology ready for clinical diagnostics?

, 2017
Bridging the “valley of death” between scientific and technological innovation and clinical implementation. Quality considerations for read mapping, variant calling and deletion mapping with Long Read Sequencing.
Taylor, Graham R., Kesia Brown, Bond, Andrew, Yau, Michael   +3 more
openaire   +1 more source

In Vivo Cytoskeletal AMPA Receptor Transport Imaging in C. elegans

Cytoskeleton, EarlyView.
ABSTRACT Long‐distance intracellular transport of ionotropic glutamate receptors (iGluRs) is essential for proper excitatory synaptic function underlying learning and memory. Many neuropsychiatric and neurodegenerative conditions have abnormal iGluR transport and trafficking, leading to an intense interest in the mechanisms and factors regulating these
Michaelis A. K., Hoerndli F. J.
wiley   +1 more source

Dynamics of Heparin Translocations Through Solid‐State Nanopores

ELECTROPHORESIS, EarlyView.
Carbohydrates can be detected with solid‐state nanopores, but their kinetics of voltage‐driven passage are fast. To better understand the dynamics of passage of these biomolecules and the role of electrophoresis and electroosmosis, we studied the translocation characteristics of heparin as a function of salt concentration, pH and voltage polarity ...
Kexin Zhao, Matthew Waugh, Kyle Briggs, Mohammad P. Jamshidi, Janelle Sauvageau, Vincent Tabard‐Cossa   +5 more
wiley   +1 more source

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

Bioinformatics, 2018
Abstract Motivation The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ format.
Alexander Payne, Nadine Holmes, Vardhman K. Rakyan, Matthew Loose   +3 more
openaire   +2 more sources