how to use NCBI sequences as sequence reference database?


I have filtered my OTU sequences according to my project criteria. Now I am in the step of “Taxonomy Assignment”, for which I want to use NCBI open source as the reference. Can someone help me finding the “qza” or any other format of this open source reference file?


Hi, I think you may have a look at MetONTIIME pipeline, and in particular at script. If you are not analysing Nanopore data, you may consider not installing the whole pipeline, and changing the source activate MetONTIIME_env line (line 47) of that script to source activate qiime2-2019.10, or whatever QIIME2 version you are running. Let me know if you suceed!

thanks a lot, will let you know.