Centrifuge SANBAFPH database for SOVAP

<strong>Centrifuge database for Sar, Nematode, Bacteria, Archaea, Fungi, Protozoa, and Human reference and representative genomes (SANBAFPH)</strong> Database type: Centrifuge database Centrifuge version: 1.0.4 Label: 17032023 Sequences: 32,318 Sum length: 25,415,962,902 Assembly summary entries: 4,668 <strong>Summary</strong> In module 2 of the SOVAP pipeline, which is dedicated to the decontamination step, we used Centrifuge software to filter out reads originating from non-viral sources. To achieve this, we created a custom database for Centrifuge called SANBAFPH, which includes reference and representative genomes of <strong>SA</strong>R (Stramenopila, Alveolata, and Rhizaria) <strong>N</strong>ematodes, <strong>B</strong>acteria, <strong>A</strong>rchaea, <strong>F</strong>ungi, <strong>P</strong>rotozoa, and <strong>H</strong>uman. This custom database enables Centrifuge to accurately identify and remove non-viral reads from the virome datasets, resulting in more accurate and reliable viral detection and analysis. -------------------------------------------------------- <strong>SOVAP v.1.3: </strong>GitHub <strong><em>Soil Virome Analysis Pipeline</em></strong> Description The study of viral communities in complex environmental samples, such as <strong>soil</strong>, can provide valuable insights into the diversity and functions of viral communities in the ecosystem. However, processing and analyzing of virome data can be a challenging task that requires the integration of various computational tools and techniques. To address these challenges, we have developed <strong>SOVAP</strong> pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data. It utilizes various tools such as <strong>Fastp</strong> and <strong>Centrifuge</strong> for preprocessing and contamination removal, <strong>geNomad</strong>, <strong>Diamond</strong> and <strong>Megan</strong> for identification and annotation of viral contigs which are assembled and clustered using <strong>Megahit</strong> and <strong>CD-HIT</strong>. Additionally, this pipeline provides an <strong>estimate of the abundance</strong> of viral contigs, allowing for a more comprehensive understanding of the virome within the sample. The integration of these tools offers a reliable and effective means of taxonomy classification and annotation of viral contigs, aiding researchers in gaining insight into the composition and function of the virome within the analyzed sample. By integrating the SOVAP pipeline with <strong>IMG/VR</strong> and <strong>geNomad</strong>, it is possible to identify a wider range of viruses, including those that were previously unknown. The <strong>batch-mode</strong> script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for <strong>large-scale</strong> analyses, such as those involving multiple environmental samples or large sequencing datasets.**针对SAR、线虫、细菌、古菌、真菌、原生动物及人类参考与代表基因组的Centrifuge数据库（SANBAFPH）** 数据库类型：Centrifuge数据库 Centrifuge版本：1.0.4 标记日期：2023年3月17日 序列数：32,318 总长度：25,415,962,902 组装汇总条目数：4,668 **摘要** 本数据集应用于SOVAP分析流程的模块2（专为污染去除步骤设计），研究团队使用Centrifuge软件过滤掉源自非病毒来源的测序读段。为此，我们构建了专用于Centrifuge的自定义数据库SANBAFPH，其包含SAR（Stramenopila, Alveolata, and Rhizaria，不等鞭毛类、囊泡虫类与有孔虫类）、线虫、细菌、古菌、真菌、原生动物及人类的参考与代表基因组。该自定义数据库可使Centrifuge精准识别并去除病毒组数据集中的非病毒测序读段，从而实现更准确可靠的病毒检测与分析。 -------------------------------------------------------- **SOVAP v1.3：土壤病毒组分析流程（Soil Virome Analysis Pipeline）**，托管于GitHub **流程说明** 对土壤等复杂环境样本中的病毒群落开展研究，可助力研究者深入理解生态系统中病毒群落的多样性与功能。然而，病毒组数据的处理与分析颇具挑战，需整合多种计算工具与技术手段。为解决上述难题，我们开发了SOVAP分析流程，该流程集成了一系列前沿工具，用于病毒组与宏基因组数据的处理、分析及注释。 该流程使用Fastp、Centrifuge等工具完成数据预处理与污染去除，使用geNomad、Diamond、Megan等工具完成病毒重叠群的识别与注释；病毒重叠群通过Megahit与CD-HIT进行组装与聚类。此外，该流程可估算病毒重叠群的丰度，帮助研究者更全面地理解样本中的病毒组构成。 上述工具的集成可为病毒重叠群的分类学注释与分类提供可靠高效的手段，助力研究者深入解析所分析样本中病毒组的组成与功能。将SOVAP分析流程与IMG/VR、geNomad相结合，可识别更多种类的病毒，包括此前未被发现的病毒。 该流程提供批量处理脚本，支持使用SOVAP对多个数据集进行统一处理。该特性尤其适用于大规模分析场景，例如涉及多环境样本或大型测序数据集的分析工作。