Global OTU table

[erifa1]

Dear all,

thanks for providing this workflow. I'm wondering if the pipeline does global clustering on overall sequences when using wildcards in --reads option (*.fastq) ? I have tested and i'm getting independent results folders for each fastq files. Is there option to get unified results as a classic OTU table that allow to compare samples.

Thanks for your help Etienne

[genomicsITER]

Hi Etienne,

Thank you for opening this issue and the suggestions. Input specification is something we would like to change in the near future and make it easier to the users when running the pipeline right after basecalling. At the moment, the --reads option only accepts bulk files containing all reads in the sample/barcode, both for --demultiplex and normal modes. You could generate this bulk file with "cat my_sample/*.fastq > mysample_bulk_file.fastq". At this time we don not know which approach to input specification is more comprehensive, but we will discuss and update this issue when the new input specification is ready

We have updated the pipeline adding abundance tables for all taxonomic levels but at this time they only cover one sample per table. We will work on providing something like an OTU table output file including all samples covered in the pipeline execution. We will update the issue when it is ready.

Regards,

Héctor

[quetjaune]

Thanks for this useful workflow. Any update on the OTU table for all samples?
Regards, Marcos