Where can I find a tutorial showing how to use beta_diversity.py (QIIME1) equivalent in QIIME2 for PERMANOVA?

[gwarmstrong (George Armstrong)]

So there is an open issue about importing CSV/TSV format directly...

This will take a couple steps:

1. Import the CSV to a biom table using biom convert. These two threads will hopefully be a good starting point.

Converting and exporting (.tsv to.biom)

Hi @conhow! Welcome! We have an open issue to support directly importing this kind of BIOM table, but for now, your workflow makes sense. Did you take a look at the BIOM docs? It looks like you should be able to run something like the following to convert your TSV BIOM file to an HDF5 BIOM file: biom convert -i table.tsv -o converted_table.biom --to-hdf5 Then, you can check out the QIIME 2 Importing tutorial for information on how to import this file! Let us know how that goes for you, …

CSV to a qiime2 readable format

Hi @coralgal! We don't currently support importing CSV or TSV formatted OTU tables. We have an open issue tracking this feature, and we'll follow up here when it's available in a release! In the meantime, you can use the biom convert tool (which comes installed with QIIME 2) to convert your CSV OTU table into a .biom file. See the biom convert tutorial for details; you'll first need to convert your CSV file to TSV. Both JSON and HDF5 versions of the .biom file format are supported by the QIIME …

2. Import the biom table with qiime tools import. See this tutorial.