LCA parameters to keep best hit only for taxonomic annotation

User Questions
1

Hi all,

I’d like to know taxonomic annotations based on only best hit species.
Which LCA parameter settings enable this?
I tried top% -> 0%, but it didn’t work like I expected.

Thank you in advance
Best,

2

Dear Penguin,

It seems you want to turn LCA off effectively - at the moment MEGAN doesn’t support that. But, you can achieve the same goal if you set your alignment tool to report only the first best hit. Than MEGAN will have no option but to use that one,

regards,
Ania

3

setting the topPercent to 0.001 will nearly do what you want, except in the case of a tie, in which case the LCA of the tied taxa will be used.