viralverify

viralVerify classifies contigs (output of metaviralSPAdes or other assemblers) as viral, non-viral or uncertain, based on gene content. Also for non-viral contigs it can optionally provide plasmid/non-plasmid classification. viralVerify predicts genes in the contig using Prodigal in the metagenomic mode, runs hmmsearch on the predicted proteins and classifies the contig as vrial or non-viral by applying the Naive Bayes classifier (NBC). For the set of predicted HMMs, viralVerify uses trained NBC to classify this set to be viral or chromosomal.