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

Abstract

Motivation: The volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use and management of public sequence (meta)data while adhering to open data principles. Results: q2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome and metagenome datasets.