How to use decontam-identify to clean table and repseqs in 2025.7?

[arwqiime (ARW)]

Hello,
I have recieved the warning about decontam-remove using q2-amplicon-2025.4. I found the following update in the 2025.7 release document.

@q2d2

@jordenrabasco removed the decontam-remove action, as this was redundant with other workflows for removing features from feature tables. You should now use qiime feature-table filter-features and qiime feature-table filter-seqs

Although decontam-remove is still working in 2025.4, I was trying to use q2 feature-table filter-features and filter-seqs as recommended. These two commands require an artifact of FeatureTable[Frequency], but q2 quality-filter decontam-identify produces an artifact of FeatureData[DecontamScore].
How should I used the output of decontam-identify to clean the abundance table and representative sequences?

Until 2025.4, I used the filtered table output from decontam-remove as an input to filter-seqs command.

Best,

[jordenrabasco]

Hi @arwqiime,

Thanks for using the plugin! To now filter features from your table you will need to use the qiime feature-table filter-features plugin, where your unaltered feature table is the input and the obj from decontam-identify output is the metadata. I will be updating the tutorial soon with the appropriate commands in the place of decontam remove. An example of the commands are below where THRESHOLD is a value between 0-1 for decontam score filtering:

Feature-Table Filtering:
qiime feature-table filter-features --i-table meta-genomic-bracken-feature-table.qza --m-metadata-file mgt_decontam_scores.qza --p-where '[p]>THRESHOLD OR [p] IS NULL' --o-filtered-table mgt_filtered_table.qza

Representative-Sequences filtering:
qiime feature-table filter-seqs --i-data representative_sequences.qza --i-table no_subset_filtered_table.qza --o-filtered-data filtered_rep_seq.qza

Let me know if you have any other questions or issues with the above commands!

best,

Jorden Rabasco

[arwqiime (ARW)]

Hi @jordenrabasco
Thank you for your explanation how to provide the decontam-scores table as a metadata-file!

Related to this a short question: My workflow to remove putative contamination hat three steps:

1. remove putativ contaminant features by (now) feature-table filter features
2. remove the control sample by feature-table filter-samples
3. remove putative contaminant sequences by feature-table filter-seqs using table from 1) and the original representative sequences.

I assume that there is no combined way to do this like the feature-table filter-feature-conditionally command, and I have to do it with the three steps above?

Best,

[jordenrabasco]

@arwqiime

ion:

Hi @arwqiime ,

Of course!

Yes to my knowledge there is not combined way to do the functionality from the three steps outlined above. The motivation for removing the command decontam-remove, was to make the workflow more applicable to QIIME 2 metagenomic workflows as well as amplicon. While this does then require more commands at the end of the day, it will hopefully make the workflow more accessible across the QIIME 2 community as a whole.

best,

Jorden