Integrating decontam with QIIME 2


I am currently a novice at bioinformatics and want to ensure that I'm doing my analysis correctly. Please let me know what option is correct:

  1. Use decontam first before importing into Qiime 2
  2. Use the output table from 'qiime dada2 denoise-paired' and input that into decontam
  3. Complete full taxonomic classification and differential abundance analysis with negative controls included in the data and then use the feature table in decontam

Thank you in advance for your help!


I guess you're trying to remove contaminants using the decontam package? If that's the case, you can go for option 2:

  1. Sequence denoising by dada2
  2. Taxonomic assignment (helpful for deciding if a feature is a contaminant).
  3. Remove contaminating features using the decontam package.
  4. Downstream analysis

For step 1 and 2, you can choose to do it in QIIME or R, depending on your preference.

You can check my code (here and here) to see how you can export the feature table, do the decontamination in R and import the filtered feature table back into QIIME.

Good luck!


Thank you so much, this was extremely helpful!