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The family <i>Morchellaceae</i> contains four truffle-forming genera: <i>Fischerula</i>, <i>Imaia</i>, <i>Kalapuya</i>, and <i>Leucangium</i>. In North America, some <i>Imaia</i>, <i>Kalapuya</i>, and <i>Leucangium</i> species are highly regarded gourmet edible fungi. In this study, we address longstanding questions about …
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 PDFAs nanopore sequencing has been widely adopted, data accumulation has surged, resulting in over 700,000 public datasets. While these data hold immense potential for advancing genomic research, their utility is compromised by the absence of …
Read PDFRestriction-modification (RM) systems are widespread defense mechanisms in prokaryotes that protect the host from potentially harmful foreign DNA. They typically consist of a DNA methyltransferase (MTase), which methylates the host genome at an adenine (6 …
Read PDF<h4>Background</h4>Nanopore technology enables the direct sequencing of intact RNA molecules allowing for the detection of native chemical modifications. In 2024, Oxford Nanopore Technologies updated direct RNA sequencing from RNA002 to RNA004 platform as well as …
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 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 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 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 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, …
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