Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data

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...

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Published in:PloS one 2015-06, Vol.10 (6), p.e0129059-e0129059
Main Authors: Daly, Gordon M, Leggett, Richard M, Rowe, William, Stubbs, Samuel, Wilkinson, Maxim, Ramirez-Gonzalez, Ricardo H, Caccamo, Mario, Bernal, William, Heeney, Jonathan L
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Assembly
Bioinformatics
Computer simulation
Contig Mapping - methods
Copy number
Data processing
DNA Contamination
DNA, Viral - chemistry
Filtration
Gene mapping
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Liver
Liver - virology
Mapping
Nucleic acids
Pathogens
Sequence Analysis, DNA - methods
Subtraction
Veterinary medicine
Viruses
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cited_by cdi_FETCH-LOGICAL-c526t-a636be63ce6dee843cc6486a36b87dbef509d1c3f170b562360c8537b0a5143b3
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creator Daly, Gordon M
Leggett, Richard M
Rowe, William
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Heeney, Jonathan L
description 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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King</contributor><creatorcontrib>Daly, Gordon M ; Leggett, Richard M ; Rowe, William ; Stubbs, Samuel ; Wilkinson, Maxim ; Ramirez-Gonzalez, Ricardo H ; Caccamo, Mario ; Bernal, William ; Heeney, Jonathan L ; Jordan, I. King</creatorcontrib><description>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. 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source Open Access: PubMed Central; Publicly Available Content Database; Coronavirus Research Database
subjects Accuracy
Algorithms
Assembly
Bioinformatics
Computer simulation
Contig Mapping - methods
Copy number
Data processing
DNA Contamination
DNA, Viral - chemistry
Filtration
Gene mapping
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Liver
Liver - virology
Mapping
Nucleic acids
Pathogens
Sequence Analysis, DNA - methods
Subtraction
Veterinary medicine
Viruses
title Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
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