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