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bioRxiv · 10.1101/2022.03.22.485322

Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue

Ziemski, M.·Adamov, A.·Kim, L.·Flörl, L.·Bokulich, N. A.
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Abstract

The volume of public nucleotide sequence data has blossomed over the past two decades, enabling novel discoveries via re-analysis, meta-analyses, and comparative studies for uncovering general biological trends. However, reproducible re-use and management of sequence datasets remains a challenge. We created the software plugin q2-fondue to enable user-friendly acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles. The software allows fully provenance-tracked programmatic access to and management of data from the Sequence Read Archive (SRA). Sequence data and accompanying metadata retrieved with q2-fondue follow a validated format, which is interoperable with the QIIME 2 ecosystem and its multiple user interfaces. To highlight the manifold capabilities of q2-fondue, we present several demonstration analyses using amplicon, whole genome, and shotgun metagenome datasets. These use cases demonstrate how q2-fondue increases analysis reproducibility and transparency from data download to final visualizations by including source details in the integrated provenance graph. We believe q2-fondue will lower existing barriers to comparative analyses of nucleotide sequence data, enabling more transparent, open, and reproducible conduct of meta-analyses. q2-fondue is a Python 3 package released under the BSD 3-clause license at https://github.com/bokulich-lab/q2-fondue.

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Ziemski, M., Adamov, A., Kim, L., Flörl, L., Bokulich, N. A.. 2022-03-25. Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue. https://doi.org/10.1101/2022.03.22.485322

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