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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
128 stars 33 forks source link

Mapping with Diamond v2 seems slow #110

Open ganiatgithub opened 1 year ago

ganiatgithub commented 1 year ago

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

fasnicar commented 1 year ago

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