PacBio CCS support for q2-dada2 does not behavior the same as the R version of dada2

Since PacBio CCS gives a better result according to Callahan et al., 2019
Is there a schedual for PacBio CCS support in q2-dada2? :thinking:

I have tried to create a new scripts run_dada_ccs.R in ~/miniconda3/envs/qiime2-2020.8/bin/ which is a modified copy of run_dada_single.R, some of the parameter has changed according to Callahan et al., 2019 to adapt to Pacbio CCS amplicon data.
Python scripts including __init__.py, plugin_setup.py, and _denoise.py in ~/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/ has also been modified to achieve a new denoise_ccs in q2-dada2.

Although that work well, I find the result is quiet different in the step filterAndtrim between the R cli and qiime2 cli. I have used the same data ,tested the R cli on Windows and linux, which is the same result. But they are different from the result through qiime2 cli I created, even with the same version of dada2, Rcpp and RcppParallel.

@sixvable, it seems like you’ve got two questions here.

I don’t think there’s a schedule at this time, but there has been recent discussion here, and an issue has been opened recently on q2-dada2 to the latest to the latest version of DADA2. That will at least remove some barriers to creating this functionality.

I’m not clear on your second question. If you care to clarify, it might help others provide an answers. For now, I’ve reclassified this to Other Bioinformatics Tools, because the core question seems to be about behavior of DADA2 in R (and perhaps a modified QIIME 2 environment?), rather than behavior of any supported QIIME 2 functionality. If I’m wrong about that, feel free to change it back to User Support when you clarify.

Best,
Chris :mouse2:

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Thank you, @ChrisKeefe

Seems like this discussion answer my first question! :grinning:

What I am trying to say in my second question is that I have implemented the denoise-pacbio function in my way in qiime2 but it works a little bit different from the R version even with same code and dataset. I guess I should join the discussion :joy:

Again thank you Chirs, this helps a lot!

Best,
Sixvable

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