Could you please tell me when generating phylogenetic tree for diversity analysis with SEPP, whether the reference database (plz check the link below) is for 16s only? If it is, do you have any recommendation for ITS database?
Thanks in advance!
q2-fragment-insertion should not be used with ITS data, please see these topics for specific discussion/details:
I just would like to point out that it is very difficult to generate a reliable global sequence alignment across all fungi using fungal ITS (I assume you are referring to fungi). Thus, ITS data are often not appropriate to generate global phylogenies. However, if you are only analyzing closely related taxa, e.g. within genera, you are likely okay. I’ve listed a few good references below. I am sure others will have additional insight too.
Check out the Fungal ITS analysis tutorial. …
I am running q2cli version: 2019.10.0 installed via conda
I am trying to build an ITS phylogenetic tree with
$ qiime fragment-insertion sepp --i-representative-sequences ./training-feature-classifiers_ITS/rep-seqs-dada2-ITS-without-recaps.qza --i-reference-database sh_refs_qiime_ver8_99_s_04.02.2020.qza --o-tree tree_ITS_without_recaps.qza --o-placements tree_placements_ITS_without_recaps.qza --p-threads 24
but I get the error message:
(1/1) Invalid value for “–i-refere…
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