I’m analyzing shotgun metagenomics data and have read-based relative abundance table (by tools like kraken-braken, metaphlan2 etc). I was wondering if I can use qiime2 to calculate diversity based on relative-abundance table. It seems that some metrics can be calculated from relative abundance (observed OTU, shannon index, Jaccard distance).
Do you know if it should work properly?
Any other suggestions from community members on how to approach it?
Yes, this should work fine. The alpha diversity metrics like Shannon and beta diversity metrics like Jaccard will work on any feature-abundance table (regardless if it’s relative abundance, and regardless if it’s amplicon).
Some of the metrics are phylogenetic, namely Faith’s PD and UniFrac. In this case, each feature will have to be placed somewhere on a phylogenetic tree, which is harder for shotgun metagenomics than amplicons, but not impossible.
One slight hiccup is the types are currently over-specific. So
qiime diversity alpha/beta will want a
FeatureTable[Frequency] since that is a “lowest common denominator” for all of the different measures/metrics.
@ChrisKeefe is currently working on cleaning this up by separating each into their own method so that we can have a more refined notion of the available types. In the meanwhile you would need to lie about the type which I don’t strongly recommend, but a deadline is a deadline sometimes.