A few months ago I ran some 16S sequencing data through Qiime2. I am now attempting to do some further analysis of the data using Valencia, a nearest-centroid based algorithm for the classification of human vaginal microbial community into state types based on their taxonomic composition. On the Valencia Github page, there is a section that gives instructions on how to convert Qiime2 output files to a format that is suitable for input to Valencia (listed below). These instructions ask for the ASV taxon names key and the ASV read count table. I believe that I should be able to find/export the read count table but am unfamiliar with the ASV taxon names key. Is anyone familiar with these files and can give me some clues on how to find and/or generate them? Many thanks for any help that you can provide!
qiime2 conversion script
This script takes ouput from qiime2 and converts it to a format suitable for VALENCIA. The two files expected as input are the ASV taxon names key and the ASV read count table. The expected output is a new table which contains the samples as rows and the condensed taxa as columns. This file can be used as input to VALENCIA. The second file provides a link between the original taxa names and the condensed names.
The script is run as follows:
python3 /path/to/convert_qiime.py /path/to/taxon_key.csv /path/to/asv_count_table.csv