Results 111 to 120 of about 29,607 (257)

pycoQC, interactive quality control for Oxford Nanopore Sequencing [PDF]

Journal of Open Source Software, 2019
Adrien Leger, Tommaso Leonardi
openaire   +1 more source

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling

Bioinformatics
Abstract Motivation Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment ...
Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose   +3 more
openaire   +3 more sources

DOM: Dual Optical Mapping Integrating Sequence‐Specific Barcodes and A/T Density Profiles

Small Methods, EarlyView.
Dual Optical Mapping (DOM) combines sequence‐specific barcodes and an A/T profile to generate complementary genomic signatures along single DNA molecules. The integration of sparse and dense mapping information enables accurate and confident genome mapping, facilitating reliable localization of long DNA molecules in complex genomes, including the ...
Jaeyoung Bae, Yunchul Kim, Joohee Choe, Jinhui Hong, Byoungsang Lee, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama, Seonghyun Lee, Jung Heon Lee, Kyubong Jo   +10 more
wiley   +1 more source

immunoHuMiX: A personalizable gut‐on‐chip model for unraveling human microbiome–immune interactions

VIEW, EarlyView.
The study introduces a personalized gut model that brings together human immune cells and intestinal cells to better mimic how the body interacts with microbes. This system successfully maintained both human cells and a 17‐strain probiotic community, showing consistent immune responses across different donors.
Charlotte De Rudder, Kacy Greenhalgh, Joanna Baginska, Camille Martin‐Gallausiaux, Léa Grandmougin, Rémy Villette, Mara Lucchetti, Bérénice Hansen, Marek Ostaszewski, Viacheslav A. Petrov, Koji Atarashi, Lena Weidert, Audrey Frachet Bour, Dominik Ternes, Javier Ramiro‐Garcia, Antoine Malabirade, Takeshi Tanoue, Marc Mac Giolla Eain, Elisabeth Letellier, Matthew Barrett, Jérôme Lacombe, Frederic Zenhausern, Coralie Guérin, Markus Ollert, Carole Seguin‐Devaux, Kenya Honda, Paul Wilmes   +26 more
wiley   +1 more source

Comparative Analysis of Stress Adaptation in the Yeast Microbiome of Cactus

Yeast, EarlyView.
Yeasts and related fungi isolated from cacti or nearby non‐cactus plants were characterized phenotypically and genomically, revealing differences that hint at modes of adaptation to the cactus host. ABSTRACT Together with other fungi, yeasts make up a significant component of the plant microbiome. As the planet warms, cacti expand their range.
Alya N. Hussain, Kevin T. Fotso, Michael A. McMurray   +2 more
wiley   +1 more source

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads

Genome Biology
Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly tool for noisy long reads, which achieves a high
Jiang Hu, Zhuo Wang, Zongyi Sun, Benxia Hu, Adeola Oluwakemi Ayoola, Fan Liang, Jingjing Li, José R. Sandoval, David N. Cooper, Kai Ye, Jue Ruan, Chuan-Le Xiao, Depeng Wang, Dong-Dong Wu, Sheng Wang   +14 more
doaj   +1 more source

Characterization of the dynamic microbiome evolution across thrips species

Insect Science, EarlyView.
Comprehensive survey of the microbiome in thrips. The dominant bacterial genera found in thrips include intracellular ones, such as Wolbachia and Spiroplasma, and extracellular ones, including Serratia, Pantoea, and Acinetobacter. We isolated and sequenced high‐quality genomes of two dominant symbionts, Pantoea dispersa and Serratia marcescens.
Xiaodi Hu, Zhaohui Shi, Yangwei Gao, Hanze Zheng, Lin Lin, Jian‐Ping Chen, Yong Chen, Chuan‐Xi Zhang, Yiyuan Li   +8 more
wiley   +1 more source

Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections

Microorganisms
Metagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely ...
Giovanni Lorenzin, Maddalena Carlin
doaj   +1 more source

Oxford Nanopore Sequencing [PDF]

, 2020
openaire   +1 more source

Simulation of RNA sequencIng with Oxford Nanopore Technologies

, 2018
Background Oxford Nanopore Technologies (ONT) platforms produce reads order of magnitudes longer than previous generation of sequencers such as Illumina (several tens to thousands of base pairs). The unprecedented long range information these reads provide is currently used to better solve genomic assembly.
Marchet, Camille, Lima, Leandro
openaire   +1 more source