Hello everybody, to anyone interested I recently developed a webapp using the streamlit python library, that allows users to run an analysis pipeline based on this great package qiime2, in a user-friendly manner, with integrated results visualizations. It is intended for italian speaking users and allows both secondary data analysis from raw fastq.gz data to OTU/ASV and taxonomy tables and tertiary data analysis from OTU and taxonomy and metadata tables to publication-quality data and charts. Kindly check this out on www.microbioma16s.it, please! Thank you!!
This is really cool @cami3!
I don't speak Italian, but I was able to work out the UI which is a great sign.
I did run into this issue with the "tertiary analysis" for taxonomy. I'm using the moving-pictures tutorial data (I think anyhow, I kind of just grabbed what was in a directory).
That said, the webapp's handling of this error is quite graceful.
Really appreciate that, thanks a lot! I'm glad you could figure out the UI even if not italian speaking!
The issue you encountered in the "tertiary analysis" could be related to the taxonomy file not being in the .csv/.tsv format. Perhaps it's in the .qzv format. It needs to be a plain text table with comma or tab separated fields, with rows representing features (OTUs/ASVs) and columns representing taxa levels (e.g. Kingdom, Phylum, Class etc. ...). Hope this might help!
Ah yes, I expected it to be a
FeatureData[Taxonomy] artifact like this:
taxonomy.qza (94.4 KB)
That might be worth supporting, since it's probably what QIIME 2 users would expect.
It is also probably worth adding some descriptions for what's expected in each of these uploads.
The webapp features could be explored using the sample data uploaded to the Github repo at microbiome/sample_data at main · cami3/microbiome · GitHub (there are files related to the moving pictures tutorial in the desired format). Thanks a lot for the suggestion, you're right I would take it in consideration! Although the "secondary analysis" step is intended to produce the files in the right format supported in "tertiary analysis" step.
Descriptions for what's expected in each uploads are available through the ? in the upper-right corner, though in italian and concise. Thank you again
I had missed the question mark, thanks for pointing that out!
Thanks to your advice now the app has the feature of accepting .qza OTU and taxonomy files.
THERE'S BALLOONS! This is great
The web app is available also in english!