secondary analysis

Dear Vladimir,

I am finally starting to use your pipeline and fixed a few issues at my side that were crashing step2.
I now have al expected folders but do not find how to proceed and get classification (I now ran a manual blast) as well nice bar plots and also phylogeny plots.

I expect this can be done using Qiime2 but I am still not too familiar with it and which files need be imported to create the right objects for plotting.

Would you by any chance have a tutorial explaining the next steps for visualisation to obtain results similar to the pb-16S-nf pipeline does for 16S. Ideally, an extension to your current https://next-its.github.io/ doc would be perfect with results from some test data.

Thanks in advance

Start with the current NextITS documentation, the step2 output folders, and the Qiime2 import requirements. Compare the requested classification, bar plots, and phylogeny plots with the pb-16S-nf results and document the workflow using test data; done means a newcomer can follow the tutorial from the existing outputs to those visualizations.