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Mapping with Diamond v2 seems slow #110

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ganiatgithub opened this issue May 23, 2023 · 1 comment
Open

Mapping with Diamond v2 seems slow #110

ganiatgithub opened this issue May 23, 2023 · 1 comment

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@ganiatgithub
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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
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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

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