2017
DOI: 10.1186/s12864-017-3721-7
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Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Abstract: BackgroundNext generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols.ResultsWe have developed a web-based application allowing direct upload of sequences from mult… Show more

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Cited by 22 publications
(15 citation statements)
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“…Stool samples were collected monthly from 3 months until 2 years of age. NGS viral sequences were assayed in serial stool samples using a custom offline version of Vipie 20. Vipie virus population profiling pipeline components include standard scripts for base quality, trimming, chimaera detection while de novo assembled contigs were generated via integration of local assembly methods SPAdes and Velvet 21 22.…”
Section: Methodsmentioning
confidence: 99%
“…Stool samples were collected monthly from 3 months until 2 years of age. NGS viral sequences were assayed in serial stool samples using a custom offline version of Vipie 20. Vipie virus population profiling pipeline components include standard scripts for base quality, trimming, chimaera detection while de novo assembled contigs were generated via integration of local assembly methods SPAdes and Velvet 21 22.…”
Section: Methodsmentioning
confidence: 99%
“…These results highlight VirMAP’s ability to more correctly build viral genomic reconstructions and assign viral taxonomies despite declining genomic coverage. In addition to VirMAP and the standard assembly and mapping approach, we also employed publicly available taxonomic classifiers that rely on read mapping (FastViromeExplorer 5 , VirusSeeker 8 , Kaiju 9 , and ViromeScan 3 ), contig mapping (VirusTAP 7 , VIPIE 2 ), a combination of both read and contig mapping (drVM 1 ), or marker gene mapping (MetaPhlAn2 6 ), for comparative purposes using the VMC dataset (Table 1 ). Other existing pipelines (e.g.…”
Section: Resultsmentioning
confidence: 99%
“…Viral metagenomics is a modern genomic technique used for studying viral communities in their natural habitat, without the isolation and laboratory cultivation of single species [ 170 , 171 , 172 , 173 ]. The sequencing of the genomic DNA information using metagenomics can be achieved either through the PCR amplicon sequencing or via shotgun metagenomics.…”
Section: Conventional Methods For the Identification Of Hev In Envmentioning
confidence: 99%