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<h4>Background</h4>Bacterial genome exploration and outbreak analysis rely heavily on robust whole-genome sequencing and bioinformatics analysis. Widely-used genomic methods, such as genotyping and detection of genetic markers demand high sequencing accuracy and precise genome assembly for …
Read PDF<b>Background/Objectives</b>: Intra-abdominal infections (IAIs) constitute significant clinical challenges that can rapidly progress to life-threatening conditions if not promptly diagnosed and treated. Traditional pathogen identification methodologies, predominantly culture-based, frequently necessitate extended turnaround times (TATs) and exhibit …
Read PDFBACKGROUND: Infective endocarditis (IE) poses significant diagnostic challenges, particularly in blood culture-negative cases where fastidious bacteria evade detection. Metagenomic-based nanopore sequencing enables rapid pathogen detection and provides a new approach for the diagnosis of IE. …
Read PDFRestriction-modification (RM) systems contribute to genome plasticity in <i>Mycoplasma hominis</i>, a facultative pathogen with an extremely small but highly heterogeneous genome. The <i>Mho</i>VII RM system, which contains a fusion of two methyltransferases (MTases), M1 and …
Read PDFThe mass rearing of insects for food and feed is increasing significantly, but it presents challenges in detecting and characterizing pathogens which may cause severe economic losses. Much attention is placed on detecting viruses, bacteria …
Read PDF<h4>Background</h4>Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet …
Read PDF<h4>Motivation</h4>Single-molecule assays like NOMe-seq, dSMF, and Nanopore are superior to DNase-seq and ATAC-seq as they do not destroy DNA. Thus, they enable quantification of all three, that is, protein-free, Transcription Factor-bound, and histone-complex-bound states. But …
Read PDFPseudomonas syringae complex (Psc) causes bacterial blight and canker on blueberry and other fruit crops. Reliable and cost-effective pathogen detection is essential for managing crop diseases. The Oxford Nanopore MinION has emerged as a powerful …
Read PDFWe report the antimicrobial susceptibility profile and genomic features of the <i>Salmonella enterica</i> serovar Rissen strain FARPER-637 isolated from Peruvian swine in 2025. Nanopore sequencing revealed blaTEM-1B, tet(A), and qnrB19. Phenotype-genotype concordance was observed except …
Read PDF<h4>Summary</h4>Nanopore sequencing technology enables real-time sequencing and is widely used in rapid detection applications. However, in clinical scenarios, existing structural variant (SV) detection tools typically separate sequencing from computation, limiting their timeliness for clinical applications. …
Read PDFThis study reports an optimized in-house 2-step PCR-SSP assay for rapid, cost-effective detection of <i>HLA-B*57:01</i> and <i>HLA-B*58:01</i> in routine pharmacogenomics laboratory. This assay employs allele-specific primers positioned within exon 2-3 boundaries, validated <i>in silico</i> against …
Read PDFThe first haplotype-resolved chromosome-scale genome assembly for the bighead catfish (Clarias macrocephalus), a freshwater species native to Thailand and Vietnam, which has importance in aquaculture and conservation, is presented here. The 880 Mb genome was …
Read PDFFolsomia candida (Collembola: Isotomidae) is one of the most important indicator species for soil animal studies and is widely distributed worldwide. Here, we utilized PacBio HiFi long reads, Oxford Nanopore Technologies (ONT) ultralong reads, Hi-C, …
Read PDFDNA methylation is crucial for genome regulation and provides key insights into the interaction between genetics and environmental factors, offering valuable perspectives for ecological research. However, knowledge of DNA methylation patterns in nonmodel invertebrates remains …
Read PDFIn recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (<i>Linum usitatissimum</i> …
Read PDF<h4>Background</h4>Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are …
Read PDFOxford Nanopore direct-RNA sequencing, a third-generation sequencing technology, allows for the analysis of native RNA molecules in their natural cellular state. However, cellular RNA is predominantly composed of ribosomal RNA and transcripts from ubiquitously expressed …
Read PDFAs a First-Class Protected species in China, the Tibetan wild ass (Equus kiang) is endemic to the Qinghai-Tibet Plateau and exhibits remarkable adaptation to extreme high-altitude environments characterized by low oxygen, cold temperatures, and high …
Read PDFHere, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: (i) Improved variant discovery and genotyping through partial order multiple …
Read PDF<h4>Background</h4>Clonotyping of immunoglobulin heavy chain (IGH) gene rearrangements is critical for diagnosis, prognostication, and measurable residual disease monitoring in chronic lymphocytic leukemia (CLL). Although short-read next-generation sequencing (NGS) platforms, such as Illumina MiSeq, are widely …
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