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Taxonomy assignment of viral RNA

Hi, I've just assembled few fecal RNA-seq (meta-transcriptomics) data that we sequenced and found viral contigs using virsorter. I'm wondering is there a good way to assign the taxonomy of the contigs (reliable method and comprehensive db as far as such db exists). Thanks.

assembly taxa metagenomics
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written by biobiu biobiu

1 answer

  1. Blast directly
  2. IDSeq, can get viral contigs and their annotation directly.
    IDSeq : An open-source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
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written by Zhilong Jia Zhilong Jia

Thanks! As for the blast option- (1) so do you suggest to just blast the contig against a db of viral RNAs? and (2) is there a comprehensive db for fecal viral RNA? I'll take a look on the IDSeq- thanks

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written by biobiu biobiu

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