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Unveiling microbial diversity: harnessing long-read sequencing technology
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete...
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Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine
PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing...
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DNA Isolation Long-Read Genomic Sequencing in Ctenophores
Long-read sequencing has proven the necessity for high-quality genomic assemblies of reference species, including enigmatic ctenophores. Obtaining...
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A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes
BackgroundLong-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly...
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A survey of algorithms for the detection of genomic structural variants from long-read sequencing data
As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of...
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Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed...
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Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing
The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in...
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Comparative analysis of metagenomic classifiers for long-read sequencing datasets
BackgroundLong reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification...
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HiFi long-read amplicon sequencing for full-spectrum variants of human mtDNA
BackgroundMitochondrial diseases (MDs) can be caused by single nucleotide variants (SNVs) and structural variants (SVs) in the mitochondrial genome...
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Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and...
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Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines
BackgroundCervical cancer (CC) causes more than 311,000 deaths annually worldwide. The integration of human papillomavirus (HPV) is a crucial genetic...
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Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells
Vascular smooth muscle cells (VSMCs) are the major contributor to vascular repair and remodeling, which showed high level of phenotypic plasticity....
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Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing
BackgroundWhile numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have...
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Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows
BackgroundLong read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly....
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Assembling Plant Genomes with Long-Read Sequencing
Continuous improvements in long-read sequencing allow us to tackle increasingly big and complex genomes. Here we present the principles of long-read...
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Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
BackgroundLong-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher...
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A microbiome survey of contrasting potato terroirs using 16S rRNA long-read sequencing
AimsAs a consequence of the increasing impact of climate change on crop production and food security worldwide, the need to explore agricultural...
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In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants
Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in...
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Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing
Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously...
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Genome analysis of Zoysia japonica ‘Yaji’ cultivar using PacBio long-read sequencing
The Zoysia japonica plant is a warm-season turfgrass and a horticultural crop used in various places and an important genetic resource because it is...
