Tonight I watched the viral genomics webinar from KBase from July 31, 2024. Ben Allen facilitated this session. Allen shared that the tools were developed by the iVirus group. The tutorial is in the public narratives: Viral Genomics in KBase. The narrative uses data from the Global Ocean Virome project and uses KBase tools to identify and classify viral sequences. Allen started with the Import SRA File as Reads from Web app to obtain data directly from SRA records and bring into KBase. After import, quality control of reads is performed using FastQC for assessment and Trimomatic to remove lower quality reads and adapters. After that, the reads are assembled with metaSPAdes. To classify viral taxonomy, Allen used an app called “Classify Taxonomy of Metagenomic Reads with Kaiju” that was recently updated to include viral databases. The options now include the NCBI viral database and one from an ongoing project. With these updates, Kaiju can be used to classify reads directly as potential viral genomes. The next tool used was VirSorter2, which now has additional viral databases. Another feature of VirSorter2 is to include outputs for DRAM. The app has options for exporting tables to annotate and further analyze. VirSorter2 has extensive documentation available to learn what the parameters do. VirSorter2 has several parameters that can be edited to improve or focus viral sequence detection. To annotate, DRAM-v is available. VirSorter2 has several output tabs! There are absence/presence tables of functions in each contig/genome. Allen described the contig identifiers produced by Spades. There were additional tools including vConTACT2 to find hits. VirMatcher helps connect viral sequences to larger metagenomic data and potential hosts. There were several tools that I didn’t know about that could be used to explore metagenomic data. The tutorial is available and could help guide undergraduate researchers in searching for viral sequences in our samples.
