Howdy! 🙂 I've been really loving the pipeline, especially the summary report output. So have all the PIs and students I've shown the pipeline to! I had one group whose 16s data I analyzed with the pipeline and they are now doing shotgun sequencing. I used the nf-core/taxprofiler pipeline to get Bracken abundance counts followed by KrakenTools to get diversity metrics. However, we're curious if there is a way to take the output from Bracken and use that as input to produce the same graphs/visuals that the 16s pipeline produces (the boxplots with statistical metrics, etc). They really like the interactive nature of the plots from ampliseq and hoped to get the same info for their shotgun data. Is there a way to use our abundance values from Bracken to get the nice figures from the ampliseq pipeline? I had attempted to convert the Bracken abundance values to a Feature Table which I then imported into QIIME2 but I'm realizing I don't have a rooted tree object to pass in with it for things like diversity analysis. Any guidance you guys have would be greatly appreciated 🙂

I think you should ask at #C031QH57DSS if they're interested in adding this feature. You can't pass data from that pipeline into Ampliseq.

Thanks, Daniel! 🙂

However, we're curious if there is a way to take the output from Bracken and use that as input to produce the same graphs/visuals that the 16s pipeline produces (the boxplots with statistical metrics, etc).

Theoretically that should be possible, I never tried though.

I had attempted to convert the Bracken abundance values to a Feature Table which I then imported into QIIME2 but I'm realizing I don't have a rooted tree object to pass in with it for things like diversity analysis.

Some metrics require a tree, some dont. There are ways to produce specific diversity indices (instead of multiple that also require a tree) in QIIME2, e.g. with https://library.qiime2.org/plugins/qiime2/q2-diversity-lib/overview and then use the output with commands like from https://library.qiime2.org/plugins/qiime2/q2-diversity/overview to plot the results. But thats sort of out of the scope of the ampliseq pipeline 😉