Viral detection and sequencing
Viral population analysis and minority-variant detection using short read next-generation sequencing
... individual viral variants can show marked or subtle ...parallel sequencing platforms, such viral populations can now be investi- gated to unprecedented ...of sequencing-related errors that ...
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Improved detection of artifactual viral minority variants in high-throughput sequencing data
... the sequencing depth will not improve the identification of these very low frequency ( ...deep sequencing datasets as the principle of artifact identification and quantification is not based on the ...
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Sequencing Needs for Viral Diagnostics
... limited sequencing resources should be ...evaluate sequencing needs using simu- lations and random sampling of existing sequence ...NN sequencing may still be war- ranted or if diminishing returns ...
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Standards for Sequencing Viral Genomes in the Era of High Throughput Sequencing
... of viral stocks. HT sequencing provides a powerful method for not only detecting the presence of contaminants within a sample but also for identification and characterization of any ...of sequencing ...
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A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
... Virus Detection Technologies Interest Group (AVDTIG) (34) that focused on identifying the strengths and weaknesses in databases, we undertook the development of a new, comprehensive RVDB that would facilitate HTS ...
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Metagenomic sequencing for surveillance of food- and waterborne viral diseases
... WATERBORNE VIRAL DISEASE Given the number of different viral pathogens potentially associated with food- and waterborne transmission their detection has not been ...
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Sequencing viral genomes from a single isolated plaque
... AE004091] (i.e., the host genome) with Phage_Finder [15] predicted prophage regions masked out. Sequence assembly and mapping The resulting cleaned-up reads were assembled using Newbler GS De Novo Assembler with minimum ...
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Clinical and biological insights from viral genome sequencing
... that detection of viral nucleic acid does not necessarily identify the cause of illness, and it is good practice when using NGS methods for diagnosis of viral infections to confirm the findings with ...
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Clinical and biological insights from viral genome sequencing
... the sequencing of either the total RNA or a subset of RNA extracted from a sample (cerebrospinal fluid or brain biopsy, for example), converted to cDNA and ...simultaneous sequencing of DNA and RNA by ...
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Efficient error correction for next-generation sequencing of viral amplicons
... The highly non-random nature of 454-sequencing errors calls for internal controls tailored to the amplicon of inter- est. The error distribution of single-clone samples helped us to calibrate the ET algorithm, ...
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The use of next generation sequencing in the diagnosis and typing of viral infections
... Until recently only a small number of respiratory pathogens were recognised and tested for. The methods used in their diagnosis required high levels of expertise, lacked sensitivity and resulted in long turnaround times ...
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Accurate Viral Population Assembly From Ultra-Deep Sequencing Data
... the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing ...
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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
... next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral ...
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System To Assess Genome Sequencing Needs for Viral Protein Diagnostics and Therapeutics
... for detection and ...for detection assays and therapeutics or as targets for vaccine ...the Sequencing Analysis Pipeline ...candidates. Viral species differ substantially in the number of ...
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Comprehensive Detection and Serotyping of Human Adenoviruses by PCR and Sequencing
... based on conserved sequences bracketing the HVR-7 of the hexon gene. Depending on the species, our sensitivity was estimated at between 200 and 4 genome copies; the latter value was obtained for the species F and, given ...
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Detection of Emerging Vaccine Related Polioviruses by Deep Sequencing
... However, VP1 mutations commonly found in VDPV outbreak strains were detected (25). These mutations alter amino acids in VP1 surface determinants and are subject to strong selection during viral replication in the ...
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Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data
... [14], the VirusSeq pipeline [5] implemented in their study uses 1,000 reads as a cutoff for virus detection. In our case, the number of identified reads was far below 1,000 for all transcriptomes, except two ...
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Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis
... of viral infections in clinical ...capture sequencing platform for vertebrate viruses (VirCapSeq-VERT) that increases the sensitivity of sequence-based virus detection and ...207 viral taxa ...
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Viral diagnostics in plants using next generation sequencing : Computational analysis in practice
... virus detection using RNA-seq requires fast and robust bioinformatics methods to enable host sequence removal and virus ...virus detection in a variety of crop plants are discussed with specific emphasis on ...
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Interpreting viral deep sequencing data with GLUE
... deep sequencing reads into Sequence Alignment Mapping (SAM) ...deep sequencing dataset obtained from a cohort of 241 UK HCV patients for whom prior treatment with direct-acting antivirals has failed; deep ...
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