ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

ABSTRACT

Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.

KEYWORDS:

• Virome
• microbiome
• bacteriophages
• bioinformatics
• metagenomics

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contributions

J.R. developed the software. M.K.M. and J.R. drafted the manuscript. J.R and X.P. performed the analyses. J.X. wrote the documentation. M.K.M. and L.D. conceived and supervised the project. All authors reviewed and approved the manuscript.

Data and software availability

ViroProfiler is available at https://github.com/deng-lab/viroprofiler. The development version of the pipeline will be updated once the dependent software are updated. The stable version will be updated yearly. The R package vpfkit is available at https://github.com/deng-lab/vpfkit. All data and reproducible analysis scripts used in this study are available as an R package at https://github.com/deng-lab/vpfpaper.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2192522.

Additional information

Funding

This work was funded by the German Research Foundation (D.F.G. Emmy Noether program, Project No. 273124240, SFB 1371, Project No. 395357507), Marie Sklodowska-Curie Actions Innovation Training Networks grant agreement no. 955974 (VIROINF), and the European Research Council Starting grant (ERC StG 803077) awarded to L.D. J.R was supported by the China Scholarship Council (CSC).