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We characterized the 4.8 Mbp genome of <i>Escherichia coli</i> H1G2, a B1 lineage isolated from the gut of Bangladesh's national fish, Hilsa (<i>Tenualosa ilisha</i>). The complete assembly reveals specialized genes for sugar metabolism and adhesion, …
Read PDF<h4>Background</h4>Targeted next-generation sequencing has emerged as a rapid solution for diagnosing drug-resistant TB (DR-TB) directly from clinical specimens. Updating the bioinformatics software component can lead to rapid improvements in diagnostic performance. We compared the diagnostic …
Read PDFPlasmids are ubiquitous tools in molecular biology which are used for a large variety of experiments within academic and commercial labs. Both new and old plasmids have to undergo sequencing-based analysis to determine whether or …
Read PDFBovine mastitis remains a major impediment to optimal dairy production. Somatic cell count (SCC) is commonly used as an indicator of mammary gland inflammation, while milk microbiota may also reflect mastitis-related changes. Here, we employed …
Read PDF<h4>Motivation</h4>Efficient data compression is crucial for reducing storage and transmission costs associated to vast volumes of nanopore raw sequencing data. Surpassing the state-of-the-art compression performance has been challenging, and all recent progress in this direction …
Read PDF<h4>Motivation</h4>Nowadays, DNA methylation in bacteria is studied mainly using single-molecule sequencing technologies like PacBio and Oxford Nanopore. In nanopore sequencing, calling of methylated positions is provided by special models implemented directly in basecallers. Prokaryotic DNA …
Read PDF<h4>Background</h4>The high error rate associated with Oxford Nanopore sequencing technology adversely affects demultiplexing. To improve demultiplexing and reduce unclassified reads from nanopore sequencing data, we developed MysteryMaster, a demultiplexer that utilizes the optimal sequence aligner, …
Read PDFBloodstream infections (BSIs) are life-threatening and require rapid, accurate pathogen characterization to guide antimicrobial therapy. Conventional culture-based diagnostics offer limited insight into the genetic basis of antimicrobial resistance (AMR) and virulence. In this study, we …
Read PDFNext Generation Sequencing is a constantly evolving technology whose applicability is increasingly expanding into the field of routine food analysis. In this context, metabarcoding has proven to be a powerful tool for detecting food fraud …
Read PDFA small cold-water teleost endemic to Northeast Asia, Hypomesus nipponensis possesses a short lifecycle, high fecundity, and rapid population growth, with extensive introductions for aquacultural purposes across East Asia. In this study, we generated a …
Read PDFThis data paper describes bacterial and fungal communities associated with the sponge <i>Chondrilla nucula</i> collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected …
Read PDF<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 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 …
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