VirProf is a dual RNA-seq analysis pipeline integrating host expression profile generation with virus identification, quantification, and genome recovery from host tissue RNA sequencing data. VirProf combines an unguided metagenomic assembly workflow with interleaved host read depletion followed by BLAST based binning, scaffolding and classification. Application of VirProf to poly-A selected RNA-seq data from nasal swabs with respiratory virus qPCR data, revealed that VirProf was able to a) quantify a range of viral infections at detection limits and precision comparable to qPCR and b) recover complete, accurate viral genomes suitable for phylogenetic analysis.