GTDB-Downloader

Tool to download GTDB samples

Description

This tool automates the download of bacterial genomes from the GTDB (Genome Taxonomy Database) via NCBI accession. . It retrieves genome assembly accessions matching a given taxonomic rank and name and gtdb_representative status, then uses the NCBI Datasets CLI tool to download corresponding genomic data. It automatically download (and store) datasets tool and GTDB database. It provides dry run and requre user confirmation before downloading samples.

Dependendencies

• R
• data.table R package (should be installed automatically)
• R.utils R package (should be installed automatically)

Required

• -n, --name: Taxonomic GTDB name, NCBI name, taxid or species taxid to query (e.g., "Escherichia coli", "562")

Optional

• -t, --taxrank: Taxonomic rank (default: "species") Options: "phylum", "class", "order", "family", "genus", "species"
• -r, --representative_check: Filter GTDB representative genomes (default: "t") Options: "t" (yes), "f" (no)
• -m, --domain: Biological domain (default: "bacteria") Options: "bacteria", "archaea"
• -o, --output_dir: Output directory (default: "output")
• -r, --report: Create a report with each sample accession number and taxonomy (flag, no value needed)
• -d, --dryrun: Preview without downloading (flag, no value needed)
• -db, --database: Custom GTDB metadata path
• -dp, --dataset_path: Path to NCBI dataset tool (not required)
• -ni, --non_interactive: Do not ask for confirmation before downloading genomes (flag, no value needed)

Example Commands

./fasta_extractor.R -n "Pseudomonas aeruginosa" -t species -r t

Acknowledgments

This tool utilizes metadata from GTDB release 226 and NCBI Datasets to access NCBI genome repository. We acknowledge the valuable contributions of the GTDB and NCBI teams in providing these resources.