Hi, is it possible to run several metrics at once? for example something like: qiime diversity alpha \ --i-table table.qza \ --p-metric shannon,observed_otus,goods_coverage \ --o-alpha-diversity metrics.qza above doesn't work :slight_smile: thanks!

As the following also doesn't work, qiime diversity alpha \ --i-table table.qza \ --p-metric shannon \ --p-metric pielou_e \ --o-alpha-diversity out what I do is a simple bash for loop: for i in shannon pielou_e do qiime diversity alpha --i-table table.qza --…

and then we need to merge output .tsvs to merged.tsv bleeee, :slight_smile:

I am using Jupyter lab to combine with Python (I don't know bash commands) variants = ['All', 'Root-Gall', 'Infected'] for variant in variants: core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant outdir = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant #Alpha diver…

Multiple metrics in a single command (qiime diversity alpha)

User Support

thermokarst February 6, 2020, 1:43pm 5

Hey @timanix, I suggest you check out the Artifact API, it will provide a much more convenient way for working with QIIME 2 in a python environment:

https://docs.qiime2.org/2019.10/interfaces/artifact-api/