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<h4>Background</h4>Cannabis powdery mildew, caused by the fungal pathogen Golovinomyces ambrosiae, poses a significant threat to licensed producers as its presence on marketable products can compromise product innocuity. While there is a focus in research for …
Read PDF<h4>Background</h4>Next generation sequencing (NGS) remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, …
Read PDF<h4>Summary</h4>Nanopore sequencing measures ionic current as native DNA or RNA molecules move through a biological pore. The resulting ionic current changes are inferred into sequence by Oxford Nanopore Technologies' Dorado basecaller. These data permit direct …
Read PDF<i>Vreelandella</i> is a genus of halophilic and Gram-negative bacteria belonging to the family <i>Halomonadaceae</i> (<i>Pseudomonadota</i>). Various genomes of this genus are currently available but their quality is uneven. Hybrid sequencing is now a common practice …
Read PDFWe report complete genome sequences of three <i>Bradyrhizobium</i> strains isolated from root nodules of peanut cultivar Tainan Select No. 9 collected in Taiwan. Hybrid assemblies using Nanopore and Illumina reads produced circular chromosome and plasmid …
Read PDF<h4>Premise</h4>Advances in long-read sequencing offer new possibilities to investigate haplotype diversity across multiple genes in plants and other taxa through multi-locus, long-read amplicon sequencing (multi-locus LRAS). Despite this progress, there is a notable absence of …
Read PDFWe report complete genome sequences of 12 <i>Azospirillum</i> strains generated using a hybrid Oxford Nanopore-Illumina sequencing approach. High-quality assemblies reveal the full multi-replicon structure of each genome, providing a valuable resource for comparative genomics, taxonomy, …
Read PDF<h4>Introduction</h4>Cystic fibrosis (CF) is an autosomal recessive disease resulting from pathogenic CF transmembrane conductance regulator (<i>CFTR</i>) pathogenic gene variants. While CF's frequency varies among ethnicities, its epidemiology, clinical manifestations, and mutational profiles in Africa still …
Read PDFFood safety is a key concern in the European Union, with the harmonisation of risk assessment methodologies being a strategic priority. The EU-FORA programme, coordinated by EFSA, promotes standardised approaches to microbial risk assessment across …
Read PDFThis article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: <i>filter_ONT</i> for filtering raw reads and creating a FASTQ file with a subset …
Read PDFCiona savignyi is an important model organism across multiple disciplines, including developmental biology, ecology, evolution, and invasion science, and has become increasingly valuable for elucidating the genomic basis of adaptation in a rapidly changing world. …
Read PDFNanopore sequencing has emerged as a promising technology due to its real-time data acquisition, portability, and high throughput. However, the genotyping capabilities of the latest flow cell, R10.4.1, for short tandem repeats (STRs) remain insufficiently …
Read PDFWe present the whole-genome sequence of <i>Escherichia coli</i> DH5α, a laboratory strain integral to molecular biology applications. We assembled a high-quality genome using Qiagen's DNeasy Blood and Tissue Kit and the Oxford Nanopore MinION platform …
Read PDFIn this study, we comparatively assessed short-read (Illumina), long-read (Oxford Nanopore Technologies, ONT), and hybrid (Illumina + ONT) sequencing strategies for bacterial genome analysis using the aquaculture-derived isolate 160P. Genomic DNA was extracted and sequenced …
Read PDFStudying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the …
Read PDFAlthough fungal eye infections are a major cause of visual impairment worldwide, standard clinical laboratory methods remain slow, insensitive, and limited in their taxonomic resolution. Sequencing of the full ribosomal RNA (rRNA) operon provides a …
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Read PDFBACKGROUND: ONT sequencing has been previously evaluated for its ability to detect plant viruses and viroids. Its advantages, such as longer read lengths and real-time analysis, compete with extensively validated Illumina platforms for possible incorporation …
Read PDF<h4>Motivation</h4>Oxford Nanopore (ONT) sequencing allows for the direct detection of RNA and DNA modifications from unamplified nucleic acids, which is a significant advantage over other platforms. However, the rapid updates to ONT basecalling models and …
Read PDFThe development of long-read sequencing technologies has enabled the analysis of extended nucleic acid sequences. These methods have proven their strength through their capacity to generate long reads, facilitating the analysis of complex genomic regions …
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