Diamond NCBI Genbank Viral database for SOVAP

<p><strong>Diamond NCBI Genbank Viral database</strong></p> <p>Database type:&nbsp;Diamond database</p> <p>Database format version:&nbsp;3</p> <p>Label:&nbsp;2023-03-18_18-40-17</p> <p>Sequences:&nbsp;3,191,190</p> <p>Sum length: 824,564,244</p> <p>Assembly summary entries:&nbsp;58,201</p> <p>--------------------------------------------------------</p> <p><strong>SOVAP v.1.3:&nbsp;</strong><a href="https://github.com/poursalavati/SOVAP">GitHub</a></p> <p><strong><em>Soil Virome Analysis Pipeline</em></strong></p> <p>Description</p> <p>The study of viral communities in complex environmental samples, such as&nbsp;<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.</p> <p>To address these challenges, we have developed&nbsp;<strong>SOVAP</strong>&nbsp;pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data.</p> <p>It utilizes various tools such as&nbsp;<strong>Fastp</strong>&nbsp;and&nbsp;<strong>Centrifuge</strong>&nbsp;for preprocessing and contamination removal,&nbsp;<strong>geNomad</strong>,&nbsp;<strong>Diamond</strong>&nbsp;and&nbsp;<strong>Megan</strong>&nbsp;for identification and annotation of viral contigs which are assembled and clustered using&nbsp;<strong>Megahit</strong>&nbsp;and&nbsp;<strong>CD-HIT</strong>. Additionally, this pipeline provides an&nbsp;<strong>estimate of the abundance</strong>&nbsp;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.</p> <p>By integrating the SOVAP pipeline with&nbsp;<strong>IMG/VR</strong>&nbsp;and&nbsp;<strong>geNomad</strong>, it is possible to identify a wider range of viruses, including those that were previously unknown.</p> <p>The&nbsp;<strong>batch-mode</strong>&nbsp;script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for&nbsp;<strong>large-scale</strong>&nbsp;analyses, such as those involving multiple environmental samples or large sequencing datasets.</p>