Fig. 1

MiCoP workflow. Reads are first aligned to viral or eukaryotic genomes in a reference database using BWA-MEM. The results provide coverage and read mapping quality information that can be examined. In the abundance estimation stage, uniquely-mapped reads are assigned to species and species abundances are estimated based on these. Multi-mapped reads are then assigned to genomes with probability proportional to their abundances among uniquely-mapped reads. Species with not enough reads mapped are filtered out, and then the final species abundances are computed