Hello @f.asnicar
I used add_viruses flag for my samples and it gave very peculiar result for just one sample as compared to results of other samples. For a particular sample it is giving me 84% relative abundance for a Micobacterium phage but when not using add_viruses for that sample I get 95% bacteria. Please explain why is that happening. Also in all other samples I have added the virus flag but it gave reasonable result which is detecting almost under ~20% viral diversity. What is the explanation for this?
Thanks
Saraswati Awasthi