FAIR meta-analyses of nucleotide sequence data with <i>q2-fondue</i>
Creators: name: Adamov, Anja
name: Ziemski, Michal
name: Kim, Lina
name: Flörl, Lena
name: Bokulich, Nicholas A
Publisher: name: F1000 Research Limited
Year: 2023

description: Given the increase in freely available nucleotide sequence data and associated metadata in the past few years, reproducibility and traceability in the conduct of meta-analyses has gained in importance. One popular platform for accessing sequence data and metadata freely is the NCBI Sequence Read Archive (SRA) that has amassed petabytes of data since its founding in 2009. To avoid manual data retrieval steps, tools have emerged that allow programmatic access to nucleotide sequence data, such as NBCI’s <i>sra-tools</i> toolkit for fetching raw sequence data and the <i>entrezpy </i>library that enables data download from NCBI’s Entrez databases. However, users with limited programming skills are hindered in adopting these existing tools due to their complex setup requirements. Additionally, since these existing tools were developed independently, they do not support consistent workflows capable of tracking every data retrieval and analysis step performed. To overcome these bottlenecks, we developed <i>q2-fondue </i>(Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere), an open-source Python package, that facilitates an efficient and transparent download, management and analysis of sequence data and metadata obtained from the SRA.<br> <br> <i>q2-fondue</i> provides a standardized approach to fetch and analyze sequence (meta)data from the SRA while following Findable, Accessible, Interoperable and Reusable (FAIR) Guiding Principles. Users can fetch their data with <i>q2-fondue </i>by either providing a list of accession IDs or a Zotero web library collection from which accession IDs can be scraped. The sequence and metadata fetched with <i>q2-fondue </i>is outputted in a validated and standardized format that is compatible with the widely adopted, fully open-source QIIME 2 ecosystem. Besides offering a standardized approach to fetch and analyze sequence (meta)data, <i>q2-fondue</i> further ensures that every data fetching and analysis step is recorded in provenance which is stored together with every single output.<br> The compatibility of <i>q2-fondue</i> with various QIIME 2 user interfaces ensures its accessibility for users possessing a range of computational skills. This integration with QIIME 2 further offers users unparalleled support through the existing QIIME 2 forum – an active exchange platform between users and plugin developers.<br> <br> <i>q2-fondue</i> is actively maintained to ensure ongoing functionality and is continually developed to address the community's evolving needs for additional features. All the existing and newly added capabilities are demonstrated through examples in the ReadMe file and a user-friendly tutorial on the project's GitHub webpage. The goal is for <i>q2-fondue</i> to become the preferred tool for interacting with the SRA and similar repositories, seamlessly integrating with the entire QIIME 2 ecosystem and enabling a diverse array of analysis types.