Hello,

Does anyone know how to analyze a large number of FASTQ files from different datasets on NCBI to generate an abundance table? I tried using DADA2, but since it requires running separately for each dataset due to the error model, I am looking for a more automated solution. I found Ampliseq from Nextflow, but it is designed to run multiple datasets from the same technique and DNA extraction method.

I was considering using the OTU instead of the ASV construction method. But, I am not sure if using OTU construction would allow me to process all different datasets in a single run.

Does anyone have suggestions or know of a method to handle this?

Thank you!