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

Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom.

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.

No MeSH data available.


Related in: MedlinePlus

Reports of novel animal virus species in PubMed over the last two decades.
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pone.0129059.g001: Reports of novel animal virus species in PubMed over the last two decades.

Mentions: Next generation sequencing (NGS) platforms offer exceptional depth, speed and accuracy of sequencing, resulting in a significant increase in the rate of new pathogen sequences that have been identified from tissues or fluids [Fig 1]. The decline in sequencing costs [1] now makes this technology broadly accessible, with some recent viral discoveries having potential health and economic benefits [1–5]. NGS is also useful as an unbiased tool with the ability to identify previously undetected or unsuspected causative agents without prior information and has the potential to become a diagnostic tool overcoming inherent a priori limitations of conventional molecular diagnostics such as PCR and microarray technology.


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

Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL - PLoS ONE (2015)

Reports of novel animal virus species in PubMed over the last two decades.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476701&req=5

pone.0129059.g001: Reports of novel animal virus species in PubMed over the last two decades.
Mentions: Next generation sequencing (NGS) platforms offer exceptional depth, speed and accuracy of sequencing, resulting in a significant increase in the rate of new pathogen sequences that have been identified from tissues or fluids [Fig 1]. The decline in sequencing costs [1] now makes this technology broadly accessible, with some recent viral discoveries having potential health and economic benefits [1–5]. NGS is also useful as an unbiased tool with the ability to identify previously undetected or unsuspected causative agents without prior information and has the potential to become a diagnostic tool overcoming inherent a priori limitations of conventional molecular diagnostics such as PCR and microarray technology.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom.

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.

No MeSH data available.


Related in: MedlinePlus