I am working with bacterial viral classification of RNAseq reads and have tried Kraken https://ccb.jhu.edu/software/kraken/ But its not giving good results.Its missing the viruses that are known thats present in the samples and have been detected by Fusion catcher as well.(Although fusion catcher is for fusion detection but it also gives viral reads information)
I have tried installing SURPI , but it took a lot of time to install it and eventually gave up on it. http://chiulab.ucsf.edu/surpi/
Any other software suggestions for this purpose?