CAPTVRED:从基于捕获的元基因组学样本中自动追踪和发现病毒的管道。

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Bioinformatics advances Pub Date : 2024-10-08 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae150
Maria Tarradas-Alemany, Sandra Martínez-Puchol, Cristina Mejías-Molina, Marta Itarte, Marta Rusiñol, Sílvia Bofill-Mas, Josep F Abril
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引用次数: 0

摘要

摘要:靶标富集测序或基于捕获的元基因组学已成为复杂样本中病毒元基因组学的一种有效方法。然而,这些数据集通常都要进行标准的下游生物信息学分析。CAPTVRED(基于捕获的元基因组学分析管道,用于从环境数据集中追踪病毒物种)旨在评估复杂样本中存在的病毒群,尤其侧重于通过目标富集测序方法获得的样本。这项工作旨在提供一种用户友好型工具,对这种测序方法进行补充,以描述全部或部分病毒群,尤其是环境基质中的病毒群。该工具包括一个设置模块,可针对一组感兴趣的物种准备和调整管道,以适应任何捕获面板。该工具还旨在减少时间和计算成本,并提供全面、可重复和可访问的结果,同时易于安装、设置和安装:源代码和测试数据集可在 github 存储库中免费获取:https://github.com/CompGenLabUB/CAPTVRED.git。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples.

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.

Availability and implementation: Source code and test datasets are freely available at github repository: https://github.com/CompGenLabUB/CAPTVRED.git.

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