Journal Article

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

Kramna, Lenka, Lin, Jake, Cinek, Ondrej, Hyöty, Heikki, Autio, Reija, Nykter, Matti

2017

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Abundance / Animal Genetics and Genomics / Applications programs / Archives & records / Assembly / Biomedical and Life Sciences / Comparative and evolutionary genomics / Dark matter / Data search / Deoxyribonucleic acid / DNA / Gene mapping / Genetic Variation / Genomes / Genomics / Genomics - methods / High-Throughput Nucleotide Sequencing / Humans / Internet / Life Sciences / Metagenomics / Microarrays / Microbial Genetics and Genomics / Microbiota - genetics / Next-generation sequencing / NGS analysis / Parallel processing / Plant Genetics and Genomics / Population / Proteomics / Quality control / Ribosomal DNA / Software / Taxonomy / Viromes / Virus / Viruses / Viruses - genetics / Visualization