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<b>Background/Objectives</b>: Advances in nanopore sequencing have opened new avenues for studying DNA methylation at single-base resolution, yet their application in epigenetic ageing research remains underdeveloped. <b>Methods</b>: We present a novel framework that leverages the unique …
Read PDFNile tilapia (<i>Oreochromis niloticus</i>) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is …
Read PDF<h4>Objectives</h4>Hygroryza aristata, an aquatic plant native to Southeast Asia, shows a high degree of adaptability to aquatic environments. H. aristata, which belongs to the Oryzeae tribe and is closely related to rice (Oryza sativa), holds …
Read PDFHuman adenovirus type 3 (HAdV-3) in the species <i>Mastadenovirus blackbeardi</i> is a frequent cause of hundreds of respiratory infections in Japan, with outbreaks varying in clinical severity. Such a high frequency of cases could be …
Read PDFThe data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained …
Read PDFNucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present a reference-guided, iterative approach to polish modification-disturbed basecalling results. We show that such an approach is uniquely …
Read PDFSoil microbiome profiling is crucial for understanding microbial diversity and its roles in ecosystem functioning and agricultural productivity. Recent advancements in high-throughput sequencing, particularly Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), offer long-read sequencing …
Read PDFNext generation long-read sequencing is a powerful approach to generate de novo genome assemblies, however it requires high-quality and high molecular weight (HMW) DNA to reach near-chromosome level assemblies. Some plants are reported as recalcitrant …
Read PDF<h4>Background</h4>Intracranial infections are severe, life-threatening conditions often caused by diverse pathogens. Targeted nanopore sequencing (TNPseq) offers rapid and accurate pathogen identification, addressing the limitations of traditional diagnostic methods. Besides the pathogen types, factors like inflammation …
Read PDF<b>Background/Objectives:</b> Massively parallel sequencing technologies have advanced chronic lymphocytic leukemia (CLL) diagnostics and precision oncology. Illumina platforms, while offering robust performance, require substantial infrastructure investment and a large number of samples for cost-efficiency. Conversely, third-generation …
Read PDFThe Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore …
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Read PDF<h4>Background</h4>Recent evidence suggests that human semen harbors a complex microbiome that may influence semen quality and male fertility. However, comprehensive characterization of bacterial and fungal communities in semen remains limited, particularly using long-read sequencing technologies.<h4>Methods</h4>In …
Read PDFFree-roaming cats may contribute to zoonotic risk via parasites and other eukaryotic taxa, yet surveillance in protected island settings is limited and conventional coprology can miss low-intensity or degraded signals. We conducted a cross-sectional 18S …
Read PDFThe identification of structural variant (SV) breakpoints plays a crucial role in understanding the genetic variants, mutagenic mechanisms, and functional consequences that drive various genetic diseases. While next-generation sequencing (NGS) has become a cornerstone in …
Read PDFBangladesh's aquaculture is currently faced with <i>Vibrio</i> contamination, which poses a threat to public health, exports, and product quality. This research provides a detailed molecular characterization of <i>Vibrio</i> sp. found in shrimp through the use …
Read PDFThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete …
Read PDFOur study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long <i>Klebsiella pneumoniae</i> outbreak with Illumina short-read sequencing data as the point of reference. We detect …
Read PDF<h4>Background</h4>Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies …
Read PDF<i>Wolbachia</i> are widespread insect endosymbionts known for manipulating host reproduction, aiding vector-borne disease control, and influencing host evolution. Here, we provide the complete genome sequence of the <i>Wolbachia</i> strain <i>w</i>Mel derived from the <i>Drosophila melanogaster</i> …
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