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Tandem repeat expansion disorders can be difficult to diagnose when expansions exceed 200 repeats, as standard methods (for example, Southern blot and modified PCR) often fail. We present a Cas9-targeted nanopore sequencing workflow and an …
Read PDFK-mer counts are fundamental in many genomic data analysis tasks, providing valuable information for genome assembly, error correction, and variant detection. State-of-the-art k-mer counting tools employ various techniques, such as parallelism, probabilistic data structures, and …
Read PDF<h4>Motivation</h4>Understanding the bacterial epigenome is increasingly recognised as essential for uncovering key mechanisms of gene regulation, host-pathogen interactions, and adaptation to environmental changes. Third-generation sequencing technologies, such as Oxford Nanopore, now enable the direct detection …
Read PDF<h4>Background</h4>Genetic testing is essential for disease screening, diagnosis, prognosis, and pharmacotherapy guidance. Oxford Nanopore Technologies (ONT) offers a cost-effective platform for long-read sequencing, yet its routine use in clinical diagnostics remains under evaluation. We tested …
Read PDFRNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses. Despite their importance, traditional detection methods-such as antibody-based enrichment, chemical labeling, or indirect sequencing approaches-often …
Read PDFChimera artifacts in nanopore direct RNA sequencing (dRNA-seq) introduce substantial inaccuracies, complicating downstream applications such as transcript annotation and gene fusion detection. Current basecalling models are unable to detect or mitigate these artifacts, limiting the …
Read PDFNanopore direct RNA sequencing holds promise for advancing our understanding of the epitranscriptome. Recently, Oxford Nanopore Technologies released basecalling models capable of detecting N6-methyladenosine (m6A), inosine (I), pseudouridine (Ψ), and 5-methylcytosine (m5C). However, their performance …
Read PDFClinical pharmacogenomics (PGx) testing strategies are mainly based on targeted PCR, microarrays, or short-read sequencing. These methods perform well for detecting known single-nucleotide variants (SNVs), small insertions/deletions (indels), and certain copy number variants (CNVs), but …
Read PDFThe assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as <i>Colletotrichum lini</i>, causing flax anthracnose disease. This study provides optimized guidelines for the T2T …
Read PDFAccurate identification of RNA 5-methylcytidine (m<sup>5</sup>C) at the single-nucleotide resolution remains a central challenge in nanopore direct RNA sequencing (DRS). Current global scanning and modification-aware basecalling methods enable transcriptome-wide profiling but often yield high false-positive …
Read PDFDiscovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) …
Read PDFWhole-genome sequencing of bacterial pathogens can positively impact infectious disease management in clinical contexts, both in individual settings and by assisting infection prevention efforts. However, logistical issues have often prevented its translation into clinical settings. …
Read PDFThe Galápagos Petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galápagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although …
Read PDFAccurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinically relevant bacterial …
Read PDF<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<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 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 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 …
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