Biomartr

Biomartr automates retrieval of genomic and metagenomic data from public repositories and annotates sequences via BioMart to support reproducible genomic and metagenomic analyses.

Key Features:

• Automated Data Retrieval: Automated retrieval from NCBI and EMBL-EBI of genomes, proteomes, coding sequences (CDS), GFF files, and metagenome data.
• Functional Annotation: Integration with the BioMart database for functional annotation of retrieved sequences.
• Reproducibility and Transparency: Emphasizes reproducibility and transparency in data retrieval and annotation through standardized functions and protocols.
• Bulk and Targeted Retrieval: Supports both bulk download of genomic datasets and targeted extraction of specific sequences or file types.
• Implementation: Distributed as an open-source R package.

Scientific Applications:

• Metagenomic studies: Automated retrieval and annotation of metagenome data to enable large-scale functional profiling and comparative analyses.
• Microbial ecology: Acquisition and annotation of genomes, proteomes, and CDS to support community composition and function studies.
• Evolutionary biology and genomics: Retrieval of genomic sequences and GFF annotations to facilitate comparative genomics and evolutionary analyses with reproducible datasets.

Methodology:

Automated data retrieval from NCBI and EMBL-EBI (genomes, proteomes, CDS, GFF, metagenome data) and functional annotation via BioMart, implemented using standardized protocols for data retrieval and annotation.