ViromeXplore: integrative workflows for complete and reproducible virome characterization

Area of Science:

• Environmental microbiology
• Bioinformatics
• Virology

Background:

• Viruses significantly influence microbial communities and biogeochemical cycles.
• The genetic diversity of viruses is vast but remains largely underexplored.
• Current viral metagenomic (virome) analysis workflows lack modularity and integration.

Purpose of the Study:

• Introduce ViromeXplore, a modular Nextflow framework for efficient virome analysis.
• Provide a scalable, user-friendly, and computationally efficient solution for viral metagenomics.
• Enhance the understanding of viral ecology through improved data analysis.

Main Methods:

• Developed modular Nextflow workflows for virome analysis.
• Incorporated tools for contamination estimation, viral identification, taxonomic assignment, functional annotation, and host prediction.
• Utilized Docker and Singularity for containerization, ensuring reproducibility and deployment ease.
• Offered optional integration with QIIME 2 and MOSHPIT for enhanced interoperability.

Main Results:

• ViromeXplore provides a comprehensive suite of tools for in-depth virome analysis.
• Optimized computational resource utilization for efficient processing of viral metagenomic data.
• Ensured reproducibility and ease of deployment through containerization.
• Facilitated seamless integration with existing microbiome analysis platforms.

Conclusions:

• ViromeXplore significantly enhances viral metagenomic analysis capabilities.
• The framework contributes to a deeper understanding of viral ecology and function.
• ViromeXplore promotes reproducible and scalable research in viromics.