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)! :fondue:

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.

Installation and documentation

You can find the plugin with all its documentation here :scroll: . We also prepared several use case examples that can be found here :nest_with_eggs: . Finally, a great tutorial by @LenaFloerl can be found in this document :woman_teacher:.


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 :hammer_and_wrench:.

Many thanks to @adamova, @LenaFloerl, @lina-kim and @Nicholas_Bokulich for working together on this one! :clap: