It's common for bowtie2 input to not be preprocessed. From the docs: "a non-local hit policy for BowTie2 (i.e. '--bt2_ps very-sensitive') is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files." Since it's common for bowtie2 input to not be preprocessed, is there a way for metaphlan to detect this and switch the default preset to very-sensitive?
...the preliminary results aren't too crazy; the skin has a load of Pacnes, and the saliva's high on Veillonella and strep. But there's a lot of strange stuff in there too - one of the skin samples is ~90% Mycobacterium, including TB and leprae, which seems unlikely. I think some of this may be caused by the high human %, lack of filtering, and local alignment policy for bowtie2"