Data is demultiplexed or not? And DADA2 or Qiime2 as a pipeline?

[Nicholas_Bokulich]

Hi @EnyaroHatsonveski ,

As you are re-using data from SRA, it might be easier to use q2-fondue, which will download, reformat, and import to QIIME 2 in a single step. See this tutorial (and please open a new topic if you run into issues using q2-fondue):

q2-fondue: Plugin for (meta)data retrieval from SRA

q2-fondue: (meta)data retrieval from SRA made simple Hello QIIMErs! On behalf of the Bokulich Lab team I would like to present to you our brand new plugin: q2-fondue (Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere)! q2-fondue allows you to grab any sequence data from the Sequence Read Archive (SRA) and corresponding metadata, given a list of SRA run accession IDs or BioProject IDs. Naturally, the resulting artifacts can then be directly plugged into …

But otherwise you can use the "Manifest" format (see the QIIME 2 online documentation for a tutorial) to import the data that you have already downloaded.

Good luck!