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Published 20 hours ago • verified publisher icon biobakery

Mapping with Diamond v2 seems slow

Open ganiatgithub opened this issue 1 year ago • 1 comments

Hi @fasnicar

It's related to a couple of posts I made link1 link2, and also a post from you on biobakery forum. I was wondering if down grading diamond to 2.0.15 or lower versions will help? Will lower versions of Diamond be compatible with Phylophlan version 3.0.67.

Many thanks. Gaofeng

ganiatgithub avatar May 23 '23 00:05 ganiatgithub

Dear Gaofeng, PhyloPhlAn is compatible with earlier versions of Diamond, the problem is that earlier versions were faster because of a bug, so your results might be biased as not all hits will be reported by Diamonds and hence your phylogenies could result incomplete.

I hope this helps, Francesco

fasnicar avatar Aug 28 '23 06:08 fasnicar