q2-fondue

q2-fondue: Nucleotide Sequence Metadata Acquisition and Provenance Tracking

q2-fondue provides programmatic acquisition, management, and meta-analysis support for nucleotide sequence metadata by enabling reproducible retrieval of datasets from the NCBI Sequence Read Archive (SRA) with integrated provenance tracking.

Key Features:

• Provenance Tracking: Records complete data lineage from SRA download through downstream processing to ensure reproducibility and transparency.
• QIIME 2 Integration: Operates within the QIIME 2 ecosystem to manage amplicon, whole genome, and metagenome datasets for microbiome analysis.
• Data Integrity Management: Prevents data loss due to storage space exhaustion during large-scale genomic data acquisition and processing.
• Publication-Linked Retrieval: Downloads sequence (meta)data associated with specific scientific publications to support structured meta-analyses.

Scientific Applications:

• Meta-analysis of Public Sequence Data: Enables reproducible reuse and integration of amplicon, whole genome, and metagenome datasets in genomics, microbiology, and bioinformatics research.

Methodology:

Implements programmatic access to the NCBI Sequence Read Archive (SRA) for automated dataset retrieval and metadata management, with full provenance capture integrated into QIIME 2 workflows to support transparent and reproducible sequence-based analyses.