CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples
Target Enrichment Sequencing or Capture-based metagenomics has emerged as an approach of interest for viral metagenomics in complex samples. However, these datasets are usually analyzed with standard downstream Bioinformatics analyses. CAPTVRED (Capture-based metagenomics Analysis Pipeline for track...
| Authors: | , , , , , , |
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| Format: | article |
| Status: | Published version |
| Publication Date: | 2024 |
| Country: | España |
| Institution: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repository: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:2445/218027 |
| Online Access: | https://hdl.handle.net/2445/218027 |
| Access Level: | Open access |
| Keyword: | Bioinformàtica Metagenòmica Bioinformatics Metagenomics |
| Summary: | Target Enrichment Sequencing or Capture-based metagenomics has emerged as an approach of interest for viral metagenomics in complex samples. However, these datasets are usually analyzed with standard downstream Bioinformatics analyses. CAPTVRED (Capture-based metagenomics Analysis Pipeline for tracking ViRal species from Environmental Datasets), has been designed to assess the virome present in complex samples, specially focused on those obtained by Target Enrichment Sequencing approach. This work aims to provide a user-friendly tool that complements this sequencing approach for the total or partial virome description, especially from environmental matrices. It includes a setup module which allows preparation and adjustment of the pipeline to any capture panel directed to a set of species of interest. The tool also aims to reduce time and computational cost, as well as to provide comprehensive, reproducible, and accessible results while being easy to costume, set up, and install. |
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