Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2?

[Nicholas_Bokulich]

Hi @rparadiso,

@rparadiso

–i-phylogeny rooted-tree.qza (green genes tree?)

Yes just import the tree that corresponds to the reference sequences that you used (e.g., if you used the 99% ref, use the 99% OTUs tree) as a Phylogeny[Rooted] following the import instructions.

If you run into any subsequent errors with core-metrics, see this topic:

Greengenes Tree Download With Branch Lengths

Hi @Stephanieorch, The issue comes from the reroot performed on that release of Greengenes where the added branch did not get set with a length (connecting "k__Bacteria" to a common vertex with "k__Archaea"). In QIIME1, this missing length was not an issue as PyCogent's PhyloNode interpreted a missing length as 0.0 when computing phylogenetic metrics so this went unnoticed at the time of release. One way to solve this is to open the tree, set a length, and write it out. An example of doing so i…

Good luck!