FastViromeExplorer: A Pipeline for Virus and Phage Identification and Abundance Profiling in Metagenomics Data published as: https://t.co/JUd0cxcLDt @thePeerJ #biorxiv
@ctitusbrown Not sure if that's what you're after, but FastViromeExplorer (https://t.co/bct32KRFd7) uses Kallisto instead of a traditional read mapping approach for detection/quantification of virus contigs in metagenomes. It seems to work, although their benchmark is vs blast not mapping