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

Daly, Gordon M, Leggett, Richard M ORCID: 0000-0003-3044-4297, Rowe, William ORCID: 0000-0003-0384-4463, Stubbs, Samuel ORCID: 0000-0003-4175-6464, Wilkinson, Maxim ORCID: 0000-0002-4924-612X, Ramirez-Gonzalez, Ricardo H ORCID: 0000-0001-5745-7085, Caccamo, Mario, Bernal, William and Heeney, Jonathan L ORCID: 0000-0003-2702-1621 (2015) Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data. PloS one, 10 (6). e0129059-.

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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.

Item Type:	Article
Uncontrolled Keywords:	Liver, Humans, DNA, Viral, Contig Mapping, Sequence Analysis, DNA, Algorithms, High-Throughput Nucleotide Sequencing, DNA Contamination
Depositing User:	Symplectic Admin
Date Deposited:	11 Apr 2016 15:30
Last Modified:	17 Dec 2022 02:28
DOI:	10.1371/journal.pone.0129059
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3000320