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Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these …
Read PDF<h4>Background</h4>Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which …
Read PDFHere, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of …
Read PDF<h4>Summary</h4>Viral genome sequencing and analysis are crucial for understanding the diversity and evolution of viruses. Traditional Sanger sequencing is limited by low sequence depth and is labor intensive. Next-Generation Sequencing (NGS) methods, such as Illumina, …
Read PDF<h4>Motivation</h4>Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e. without basecalling). However, existing solutions cannot interpret raw signals directly if a …
Read PDF<h4>Motivation</h4>Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in …
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 PDFGenomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor …
Read PDFNanopore direct RNA sequencing (DRS) offers distinct advantages for transcriptome analysis over the traditional high-throughput RNA sequencing methods by preserving native RNA modifications, eliminating polymerase chain reaction bias, and simplifying the workflow. However, its high …
Read PDFThis dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates …
Read PDFCharting the eukaryotic epitranscriptome by direct RNA sequencing is promising but still very challenging, as current bioinformatics tools are based on modification-unaware software and require multiple modification-specific learning steps. Here, we introduce NanoSpeech, a modification-aware …
Read PDFNanopore sequencing enables real-time access to raw signal data, which brings new possibilities for rapid genomic diagnostics. However, current workflows still primarily rely on basecalling, a computationally intensive step that slows subsequent analysis and limits …
Read PDFWhile nanopore direct RNA sequencing has substantially advanced transcriptomics, its detection of RNA modifications remains primarily focused on abundant biological base modifications. However, therapeutic RNAs employ a diverse catalog of modifications, including base, sugar, and …
Read PDF<h4>Background</h4>Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor …
Read PDF<h4>Background</h4>Oxford Nanopore Technologies (ONT) sequencing enables direct, long-read sequencing of DNA and RNA, preserving nucleotide modifications. During basecalling, deep neural networks translate raw nanopore signals into nucleotide sequences, internally segmenting the signal to align it …
Read PDFNanopore sequencing is an increasingly central tool for genomics. Despite rapid advances in the field, large data volumes and computational bottlenecks continue to pose major challenges. Here, we introduce ex-zd, a new data compression strategy …
Read PDFThe integration of artificial intelligence (AI) into next-generation sequencing (NGS) has revolutionized genomics, offering unprecedented advancements in data analysis, accuracy, and scalability. This review explores the synergistic relationship between AI and NGS, highlighting its transformative …
Read PDF<h4>Background</h4>Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention …
Read PDFHigh-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing …
Read PDF<h4>Purpose of review</h4>Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public …
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