The purpose of this post if to get some guidance for making a new plugin for qiime2: we have implemented a pipeline for taxonomic annotation at species/sub-species level for the Bifidobacterium genus (based on 16s sequencing). Our process is described here: https://doi.org/10.1111/1462-2920.14274).
Technically peaking our current “Bifidobacterium species & sub-species annotation” is an R script and uses as entry point an alignment (made in mothur with the align.seqs function) of the representatives sequences (from Bifidobacterium genus) on aligned Silva database.
This alignment done in mothur with align.seqs is absolutely key and we did not find any exact equivalent in q2 (possibly the MAFTT will be updated soon but in our tests (see here) we do not obtain the same results with MAFFT (vs align.seqs).
We were wondering if we could use, in a q2 plugin, mothur as a dependency ? (or eventually only the mothur align.seqs function ?)
Thanks a lot