Hi, is it possible to only profile VSC (ignoring all bacteria, archea etc to speed up the analysis)?
I already profiled the bacteria but want a different coverage breadth for VSC and this account be done from the bowtie files.
would the parameters “–ignore_bacteria” speed up things?
Hi @Robin_Mjelle
At the moment MetaPhlAn is implemented in a way that doesn’t allow the mapping of viral sequences only, because the mapping is performed against a database which includes bacteria and phage sequences all together. Using the --ignore_bacteria would not speed up things because the mapping step, which is the bottle neck, would still be executed. I suggest you to use a lower breadth of coverage and then filter the table at different breadth of coverage if you are interested in testing different thresholds. Just be aware that a lower coverage may result in an increase in false positive phages being called