ViromeXplore: integrative workflows for complete and reproducible virome characterization.
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| Title: | ViromeXplore: integrative workflows for complete and reproducible virome characterization. |
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| Authors: | Hernández-Velázquez R; Department of Health Sciences and Technology, ETH Zurich, Rämistrasse 101, 8092 Zurich, Switzerland., Ziemski M; Department of Health Sciences and Technology, ETH Zurich, Rämistrasse 101, 8092 Zurich, Switzerland., Bokulich NA; Department of Health Sciences and Technology, ETH Zurich, Rämistrasse 101, 8092 Zurich, Switzerland. |
| Source: | Briefings in bioinformatics [Brief Bioinform] 2025 Nov 01; Vol. 26 (6). |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE |
| Imprint Name(s): | Publication: Oxford : Oxford University Press Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000- |
| MeSH Terms: | Virome* , Workflow* , Metagenomics*/methods , Software* , Computational Biology*/methods , Viruses*/genetics , Viruses*/classification, High-Throughput Nucleotide Sequencing ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results |
| Abstract: | Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore. (© The Author(s) 2025. Published by Oxford University Press.) |
| Grant Information: | 22.00210 Swiss State Secretariat for Education, Research and Innovation; European Union nor European Research Executive Agency |
| Contributed Indexing: | Keywords: Nextflow; metagenomics; viromics; virus; workflow |
| Entry Date(s): | Date Created: 20251205 Date Completed: 20251205 Latest Revision: 20251205 |
| Update Code: | 20251206 |
| DOI: | 10.1093/bib/bbaf638 |
| PMID: | 41348596 |
| Database: | MEDLINE |
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Nájsť tento článok vo Web of Science | Abstract: | Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.<br /> (© The Author(s) 2025. Published by Oxford University Press.) |
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| ISSN: | 1477-4054 |
| DOI: | 10.1093/bib/bbaf638 |