q2-dada2 FeatureData[LinkedSequence]

arwqiime · November 4, 2026, 11:17am

(topic deleted by author)

arwqiime · November 4, 2026, 12:53pm

Hello,

I have realized that the FeatureData[LinkedSeqeunce] issue has been resolved for several plugins in q2-2026.10 release. Thank you!

There is one additional plugin option, that I found incompatible with this new type:

qiime quality-control decontam-score-viz --i-rep-seqs seems to be affected, also this input is optional (no error when omitting --i-re-seqs)

Invalid value for '--i-rep-seqs': Expected an artifact of at least type
FeatureData[Sequence]. An artifact of type FeatureData[LinkedSequence] was
provided.

Best

Nicholas_Bokulich · November 5, 2026, 7:35am

Hi @arwqiime ,
Thanks for giving the new FeatureData[LinkedSequence] type a spin!

I have opened an issue to add this as an acceptable type to decontam-score-viz. You can follow this issue to track status of this feature request:

github.com/qiime2/q2-quality-control

ENH: accept FeatureData[LinkedSeqeunce] as input to decontam-score-viz

opened 07:25AM - 05 Nov 26 UTC

nbokulich

**Addition Description** Accept `FeatureData[LinkedSeqeunce]` as an acceptable i…nput type for the `rep_seqs` input of `decontam-score-viz` **Current Behavior** `FeatureData[LinkedSeqeunce]` is not a valid input to `decontam-score-viz` **Proposed Behavior** Add `FeatureData[LinkedSeqeunce]` to the list of acceptable input types for `rep_seqs` **Questions** 1. Will this action choke on any whitespace chars in the linked sequences? I have not looked yet to see how the rep-seqs are handled in this action. **References** [Requested via a forum user](https://forum.qiime2.org/t/q2-dada2-featuredata-linkedsequence/34375/2?u=nicholas_bokulich)