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 any other QIIME 2 analysis.
No more annoying shell scripts, no more faffing around with accession IDs, no more interrupted downloads! Simply provide a list of supported IDs and let q2-fondue take care of the rest.
For more details on the inner workings of q2-fondue be sure to check out our pre-print: Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue | bioRxiv.
Should you need any support, please reach out here on the forum .