Recently Decontam functionality has been added to the QIIME2 platform under the q2-quality-control umbrella.
Below are links to two different tutorials for the added Decontam functionality. The first is how to run Decontam within QIIME2, and the second is how to run a specialized action called Decontam-Batches which is designed to help track down sources of contamination in experiments. At the top of each tutorial is a description of what the tutorial entails and how to interpret the results from each action.
These tutorials are very much a work in progress please feel free to reach out to me on the forum or at jrabasc@ncsu.edu if you have any further questions or feedback!
Hi @jordenrabasco
Thank you for the Decontam tutorials. I applied it to my own data got some intersting results. I have a few (technical) questions:
I assume that the --i-rep-seqs parameter has been removed in decontam-score-viz of recent q2 releases - could this explain that there is not Decontam sequence table (and download links) in the qzv output?
A second question is related to the interpretation of the score histogram obtained with my own data: How would one investigate the 'lonely' bar (score below 0.2) of the graph below? I do not have access to the sequences, right (previous question)?
No problem, I appreciate you taking the time to look through them. Glad to hear you are interested in applying it to your own data!
What version of QIIME2 are you running? Judging by the look of the graph and table it looks like you maybe using an older version of QIIME2. The tutorial was written assuming that the most recent release of QIIME2 is being used, so if you use the latest version you will be able to see the Decontam sequence table and be able to investigate the 'lonely' bar more thoroughly.
Alternatively, i believe you can export the Decontam scores table and the representative sequences table and then investigate those seqs that have the same id as the features that have a decontam score of less than 0.2 but greater than 0.1. This would be a bit of a headache though and I would recommend just updating the QIIME2 environment, which you can do here
Hi @jordenrabasco
I am using qiime2-amplicon-2024.2. The qza data of the tutorial were created using q2-2022.2, and I was assuming that my q2 version is younger.
Best
Short update: I realized the the --i-rep-seqs is present in 2024.5, but not in 2024.2; Table and download buttons are there.
Sorry!
