Feature request: Have you thought about adding sup...
# taxprofilerr
Rasmus Hindström
11/11/2025, 10:03 AMFeature request: Have you thought about adding support for TSE (TreeSummarizedExperiment)? A similar taxonomic profiling pipeline for amplicon data (nf-core/ampliseq) supports output into a ready TSE -object, which is rather useful to transition into downstream analysis. I was wondering if similar support could be added to Taxprofiler.
j
James Fellows Yates
11/11/2025, 10:09 AMI think @moritz had thought about this before?
James Fellows Yates
11/11/2025, 10:09 AMBut feature requests via github please @Rasmus Hindström!
James Fellows Yates
11/11/2025, 10:09 AMJames Fellows Yates
11/11/2025, 10:09 AMBut I think it fits in the scope in teh pipeline 🙂
m
moritz
11/11/2025, 10:10 AMWith the taxpasta standardization, you can output BIOM format and import that as a TSE.
j
James Fellows Yates
11/11/2025, 10:10 AMAh there you go then 😉
r
Rasmus Hindström
11/11/2025, 10:10 AMAh right, I'll check if there is an open feature request and if not create one. This would be very useful as an option.
It's true that you can get the BIOM imported into a tse. But if its not a big hurdle, having the output directly into a TSE -object could still be useful for us users. :)
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