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Ciona 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 …
Read PDFRapid identification of copy-number variations (CNVs) is crucial in prenatal diagnosis; however, current chromosomal microarray analysis (CMA) has a lengthy turnaround time. We evaluated the feasibility of low-pass nanopore sequencing for genome-wide CNV detection using …
Read PDFGenome assembly from long-read sequencing data has become a standard approach for resolving complex genomic regions and producing high-contiguity assemblies. However, the diversity of available assemblers, their varying performance across species, and the need for …
Read PDF<h4>Background</h4>HIV drug resistance (HIVDR) testing remains essential for optimizing antiretroviral therapy (ART), yet access remains constrained by high cost, low throughput, and limited availability of Sanger sequencing in resource-limited settings (RLS). Recent improvements in Oxford …
Read PDFAntimicrobial resistance (AMR) poses a significant threat to public health, particularly in low- and middle-income countries where centralized genomic surveillance infrastructure is limited. To support decentralized AMR surveillance in Africa, the SeqAfrica project evaluated bioinformatics …
Read PDF<h4>Background</h4>Variants in the dentin sialophosphoprotein (<i>DSPP</i>) gene are associated with dentin dysplasia type II (DD-II; OMIM # 125420) and dentinogenesis imperfecta (DI) types II (OMIM # 125490) and III (OMIM # 125500). <i>DSPP</i> encodes a …
Read PDF<h4>Objective</h4>Although loiasis affects more than 20 million people and that its associated clinical complications can cause multiple organ failures, this disease remains understudied. Consequently, the elimination of loiasis is not on the agenda of public …
Read PDFBACKGROUND: Oxford Nanopore Technologies (ONT) workflows attach synthetic adapters and barcode oligonucleotides to DNA fragments for priming and multiplexing. Although these sequences are normally removed during basecalling or post-processing, incomplete trimming can embed non-biological fragments …
Read PDFNanopore sequencing with the MinION device has revolutionized genomic research. This study evaluated the MinION nanopore sequencer for accuracy, reliability, and reusability. Sequencing of λ phage DNA and <i>E. coli</i> DNA achieved high accuracy and …
Read PDFAccurate viral genome characterization is essential for understanding viral dynamics. Oxford Nanopore Technologies (ONT) Direct RNA Sequencing provides detailed genomic data by directly reading RNA molecules, avoiding biases from reverse transcription and PCR. However, it …
Read PDF<h4>Background</h4>Rapid and accurate whole-genome sequencing (WGS) is increasingly important for detecting antimicrobial resistance and virulence determinants in clinical microbiology. Although short-read platforms remain widely used, long-read sequencing technologies have gained relevance due to their ability …
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