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SOVAP v.1.3: GitHub

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Soil Virome Analysis Pipeline

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Description

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The study of viral communities in complex environmental samples, such as soil, 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.

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To address these challenges, we have developed SOVAP pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data.

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It utilizes various tools such as Fastp and Centrifuge for preprocessing and contamination removal, geNomad, Diamond and Megan for identification and annotation of viral contigs which are assembled and clustered using Megahit and CD-HIT. Additionally, this pipeline provides an estimate of the abundance 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.

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By integrating the SOVAP pipeline with IMG/VR and geNomad, it is possible to identify a wider range of viruses, including those that were previously unknown.

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The batch-mode script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for large-scale analyses, such as those involving multiple environmental samples or large sequencing datasets.

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