Switching analysis from USEARCH to QIIME2

QIIME2 is great and I am a fan of how easy the visualization is. That’s why I want to generate core metrics with qiime2.
I currently have an OTU table output file (in .txt format) from usearch;

  • The first column of the table is the OTU# (e.g. Zotu5, Zotu6, etc)
  • Columns two to five are the sample names (e.g. 6601, 6602, etc)
  • Rows, of course, represent the number of sequences in each sample under each OTU.

I want to convert this table to a .qza file format to be used as input for the “–i-table” flag in order to run the “qiime diversity core-metrics-phylogenetic” command.

I tried to use these flags during importing but to no avail:

  1. qiime tools import --type FeatureTable[Frequency] --input-format BIOMV210Format
  2. qiime tools import --type FeatureTable[Frequency] --input-format DistanceMatrixDirectoryFormat

Does anyone have a formula for this? Thanks. Looking forward to it.


Hi @ahmedshibl,
You’ll need to convert your .txt feature table to a biom format before importing it as per your attempt # 1.
This similar post should help you get there.

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