Hi, is there a way to run core-metrics without a phylogenetic tree, as when working with ITS sequences, or do you have to run each diversity metric separately?
Hi @Lorinda,
Unfortunately you would need to run each step separately at this time. Sorry!
The methods of interest for you will be: rarefy, alpha, beta, and pcoa from the diversity plugin. e.g. qiime diversity rarefy and so on.
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@ebolyen OK, thanks! For the beta step then, can you run multiple distance metrics at a time, i.e. braycurtis, jaccard etc. or do they each have to be run with a separate script? I would just run it myself and check, but I am still getting used to the QIIME2 language...
@Lorinda, you'll need to run it multiple times for each metric. This is definitely an area where we could improve.
Just noting that I opened an issue to track this feature. We'll follow up here when it's implemented!
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Just to update: 2017.9 is out and, core-metrics is now non-phylogenetic. We have a new method core-metrics-phylogenetic for when you have a tree.