Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11130%2F17%3A10373811" target="_blank" >RIV/00216208:11130/17:10373811 - isvavai.cz</a>

Alternative codes found

RIV/00064203:_____/17:10373811

Result on the web

<a href="https://doi.org/10.1186/s12864-017-3721-7" target="_blank" >https://doi.org/10.1186/s12864-017-3721-7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12864-017-3721-7" target="_blank" >10.1186/s12864-017-3721-7</a>

Result language

angličtina

Original language name

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Original language description

Background: Next 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. Results: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. Conclusions: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped (&apos;dark matter&apos;) reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

30209 - Paediatrics

Project

<a href="/en/project/NV15-31426A" target="_blank" >NV15-31426A: Childhood-onset diabetes in sub-Saharan Africa: genetic and virological findings in Nigeria, and their comparison to European populations</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BMC Genomics

ISSN

1471-2164

e-ISSN

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Volume of the periodical

18

Issue of the periodical within the volume

May

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

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UT code for WoS article

000401577300001

EID of the result in the Scopus database

2-s2.0-85019187859