Lytic Transcriptome Dataset of Varicella Zoster Virus Generated by Long-Read Sequencing
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Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain
RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We developed a new approach to address this challenge, …
Read PDFLongshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing
Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such …
Read PDFHigh Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (<i>Dioscorea dumetorum</i>) Using Long Read Sequencing
Trifoliate yam (<i>Dioscorea dumetorum</i>) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources …
Read PDFYes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus
<h4>Background</h4>Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' …
Read PDFDepletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (<i>Ursus maritimus</i>)
Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their …
Read PDFNoise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data
<h4>Summary</h4>Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat …
Read PDFLong-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses
Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in …
Read PDFComplete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing
<h4>Background</h4>Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. …
Read PDFDynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection
<h4>Background</h4>Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced …
Read PDFCharacterization of the genomic sequence data around common cutworm resistance genes in soybean (<i>Glycine max</i>) using short- and long-read sequencing methods
The common cutworm (CCW, <i>Spodopteraab litura</i> Fabricius) is one of the pests that most severely infect soybean (<i>Glycine max</i> L. Merr.). In a previous report, quantitative trait loci (QTL) analysis of CCW resistance using a …
Read PDFMultiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome
Long-read sequencing (LRS) has become increasingly important in RNA research due to its strength in resolving complex transcriptomic architectures. In this regard, currently two LRS platforms have demonstrated adequate performance: the Single Molecule Real-Time Sequencing …
Read PDFFirst record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach
<h4>Background</h4>Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them …
Read PDFNanoPack: visualizing and processing long-read sequencing data
<h4>Summary</h4>Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.<h4>Availability and implementation</h4>The NanoPack tools are written in Python3 and released under …
Read PDFComparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined …
Read PDFUsing long-read sequencing to detect imprinted DNA methylation
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 PDFHigh-resolution mapping of reciprocal translocation breakpoints using long-read sequencing
Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed …
Read PDFCharacterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking <i>Listeria monocytogenes</i> from Food Processing Environments
Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of <i>Listeria monocytogenes</i> (<i>Lm</i>) epidemic clone …
Read PDFUltraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
Hybrid genome assembly has emerged as an important technique in bacterial genomics, but cost and labor requirements limit large-scale application. We present Ultraplexing, a method to improve per-sample sequencing cost and hands-on time of Nanopore …
Read PDFLocation of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform
Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do …
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