ArticlePloS one2015
Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.Genome medicine · 2024Article
- NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection.Frontiers in microbiology · 2023Article
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- Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing.Microorganisms · 2021Article
- Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR.Virus evolution · 2021Article
- MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data.BMC genomics · 2020Article
- Tissue-associated microbial detection in cancer using human sequencing data.BMC bioinformatics · 2020Review
- Transcriptome-Wide Comparisons and Virulence Gene Polymorphisms of Host-Associated Genotypes of the Cnidarian Parasite Ceratonova shasta in Salmonids.Genome biology and evolution · 2020Article
- SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.Genome biology · 2019Article
- Review
- DNAscan: personal computer compatible NGS analysis, annotation and visualisation.BMC bioinformatics · 2019Article
- Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.GigaScience · 2018Article
- Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems.Frontiers in microbiology · 2018Article
- A draft genome sequence for theF1000Research · 2018Article
- A host subtraction database for virus discovery in human cell line sequencing data.F1000Research · 2018Article
- Article
- Challenges in the analysis of viral metagenomes.Virus evolution · 2016Review
- Recovering full-length viral genomes from metagenomes.Frontiers in microbiology · 2015Review
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.