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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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[FEATURE] updating diamond to the 2.0.x series #1805

Open dspeth opened 2 years ago

dspeth commented 2 years ago

The need

anvi'o uses DIAMOND in many cool functionalities, and offers selection of fast and sensitive modes. According to the recent publication on the updated version of DIAMOND (https://www.nature.com/articles/s41592-021-01101-x) its sensitive mode in the newer versions is substantially better than it is in older versions. There are also two additional sensitivity modes added (very and ultra).

The solution

Add additional sensitivity modes to relevant programs, and check compatibility of recent DIAMOND versions with other dependencies. I suspect you're already working on this, but couldn't find an open issue about it.

Beneficiaries

most anvi'o users, as DIAMOND is used in a range of anvio functinalities

meren commented 2 years ago

Thanks for this, @dspeth! We have not been working on this, but obviously we should have been! :)

I'll try to get to this at some point.