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Nanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggling in noisy regions. We present Campolina, a first …
Read PDF<h4>Background</h4>Nanopore sequencing is currently one of the leading third-generation sequencing technologies on the market and is gaining popularity among researchers. Due to its long-read capabilities, full-length 16S rRNA gene metabarcoding using Oxford Nanopore Technologies (ONT) …
Read PDFIn recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have …
Read PDFMicrobial cell-free DNA (mcfDNA) enables rapid and sensitive pathogen detection via direct plasma-sequencing. Here, we present a fast, cost-effective mcfDNA multiplex workflow to complement or improve the sensitivity of microbiological diagnostics for systemic and focal …
Read PDF<h4>Background</h4>Over the years, there has been growing interest in epigenetics, where nucleotide modifications are increasingly recognized for their roles in health and disease. Understanding methylation patterns at the nucleotide level has become pivotal for advancing …
Read PDFThe vaginal microbiota is a dynamic ecosystem that plays a central role in women's reproductive health, with Lactobacillus species typically dominating in healthy individuals. Disruptions to this microbiota can lead to dysbiosis, increasing susceptibility to …
Read PDFHuman papillomavirus 16 (HPV16) drives precursor cervical lesions that often progress to cervical cancer (CC). Variation within the HPV16 genome has been associated with CC risk. Here, we developed an affordable and portable amplicon-based long-read …
Read PDF<b>Objectives.</b> <i>Vibrio cholerae</i> remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of <i>V. cholerae</i> isolates from Côte d'Ivoire, Ghana, Zambia and South Africa …
Read PDFNanoPrePro is a streamlined read preprocessor specifically designed for high precision in identifying full-length reads from Oxford Nanopore Technology (ONT) transcriptomic sequencing results, achieved through the precise identification of adapters/primers. However, the preprocessing of ONT …
Read PDFCarpoglyphus lactis is a globally distributed stored-product pest mite that inflicts substantial damage on dried fruits, grains, and other preserved commodities. However, the absence of high-quality genomic resources has long constrained insights into its biology …
Read PDFOxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and …
Read PDFMagnolia zenii (Magnoliaceae) is an extremely endangered tree species endemic to eastern China, has only 115 individuals remaining in the wild. By integrating PacBio HiFi (49×), Oxford Nanopore (ONT; 101×) long-read sequencing, and Hi-C chromatin …
Read PDFShort tandem repeats (STRs) are repetitive DNA sequences that contribute to genetic diversity and play a significant role in disease susceptibility. The human genome contains approximately 1.5 million STR loci, collectively covering around 3% of …
Read PDFAmplicon sequencing is a popular method for understanding the diversity of bacterial communities in samples containing multiple organisms as exemplified by 16S rRNA sequencing. Another application of amplicon sequencing includes multiplexing both primer sets and …
Read PDFMobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike …
Read PDFLower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation …
Read PDFAs the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand …
Read PDFWe present a DNA extraction protocol for atmospheric bioaerosol samples collected on glass-fiber filters widely used in air quality monitoring. The protocol produces high-quality molecules suitable for third-generation sequencing and other applications. The initial protocol …
Read PDFAffordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infections or emerging …
Read PDFHistorically, antibiotic development has been driven by research into secondary metabolism which is responsible for the biosynthesis of so-called natural products. This research has been revolutionized by our growing capacity to rapidly generate and analyze …
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