Unknown

Dataset Information

0

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

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.

SUBMITTER: Daly GM 

PROVIDER: S-EPMC4476701 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

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

Daly Gordon M GM   Leggett Richard M RM   Rowe William W   Stubbs Samuel S   Wilkinson Maxim M   Ramirez-Gonzalez Ricardo H RH   Caccamo Mario M   Bernal William W   Heeney Jonathan L JL  

PloS one 20150622 6

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  ...[more]

Similar Datasets

Unknown Next Generation Sequencing of Pooled Samples: Guideline for Variants' Filtering.
| S-EPMC5037392 | biostudies-literature
Unknown Next generation sequencing: potential and application in drug discovery.
| S-EPMC3933208 | biostudies-other
Unknown A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing.
| S-EPMC3244418 | biostudies-literature
Unknown Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.
| S-EPMC8464054 | biostudies-literature
Unknown Next generation sequencing of viral RNA genomes.
| S-EPMC3708773 | biostudies-literature
Proteomics Next Generation Protein Sequencing
2017-04-03 | PXD003804 | Pride
Unknown VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.
| S-EPMC8941893 | biostudies-literature
Unknown Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery.
| S-EPMC3633874 | biostudies-other
Unknown A host subtraction database for virus discovery in human cell line sequencing data.
| S-EPMC6556987 | biostudies-literature
Unknown RetroSeq: transposable element discovery from next-generation sequencing data.
| S-EPMC3562067 | biostudies-literature