changed bowtie2 default to be very-sensitive

[karlrl]

What prompted this change? If there's a discussion elsewhere that's worth linking, let me know! 😄

[gavinmdouglas]

--very-sensitive is the current default in metaphlan2.py. A change in our wrapper to be this as well is motivated by observing many spurious hits to plant viruses in certain samples when local alignment is used and which disappear when global alignment is used.

The issue of false positives and bowtie2 settings has been discussed a bit on the metaphlan2 google group as well:

https://groups.google.com/forum/#!searchin/metaphlan-users/alignment$20setting%7Csort:date/metaphlan-users/PBhBM5aFjdk/DGG1Ifk6l3QJ

https://groups.google.com/forum/#!searchin/metaphlan-users/alignment$20setting%7Csort:date/metaphlan-users/qNGO0897Lqw/Zyflg16NCAAJ

[karlrl]

Thanks for the explanation!