Format

Send to

Choose Destination
BMC Genomics. 2017 May 15;18(1):378. doi: 10.1186/s12864-017-3721-7.

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

Author information

1
BioMediTech and Faculty of Medicine and Life Sciences, University of Tampere, PB 100, FI-33014, Tampere, Finland.
2
Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, 150 06, Praha 5, Czech Republic.
3
School of Social Sciences, University of Tampere, Kalevantie 4, 33100, Tampere, Finland.
4
BioMediTech and Faculty of Medicine and Life Sciences, University of Tampere, PB 100, FI-33014, Tampere, Finland. heikki.hyoty@uta.fi.
5
Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland. heikki.hyoty@uta.fi.
6
BioMediTech and Faculty of Medicine and Life Sciences, University of Tampere, PB 100, FI-33014, Tampere, Finland. matti.nykter@uta.fi.
7
Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, 150 06, Praha 5, Czech Republic. ondrej.cinek@lfmotol.cuni.cz.

Abstract

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 ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

KEYWORDS:

Assembly; Metagenomics; NGS analysis; Parallel processing; Viral dark matter; Viromes; Virus; Visualization

PMID:
28506246
PMCID:
PMC5430618
DOI:
10.1186/s12864-017-3721-7
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center