gdl - Genome Download

A fast, easy-to-use, command-line tool for downloading genome assemblies from NCBI GenBank (RefSeq).

Features

• Easy Taxonomic Filtering - Retrieve assemblies at or below a given taxonomic name or ID (E.g., "download all assemblies within the order Lactobacillales")
• Assembly Metadata Filtering - Specify genome completeness, source (GenBank, RefSeq), format (.gbk, .fna)
• Fast - Re-use connections and process downloads in parallel
• Portable - Distributed as a single binary executable

Examples

# Download all assemblies within the clade "Dinosauria"
gdl --tax-name Dinosauria

# Download all GenBank genomes within the order Lactobacillales
gdl --tax-name "Lactobacillales" --source genbank

# Download all complete RefSeq assemblies in .gbk format within the genus
# Phocaeicola (tax_id=821)
gdl --tax-id 821 --format gbk --source refseq --assembly-level "Complete Genome"

# Download all Betacoronavirus genomes in GenBank
gdl --tax-name "Betacoronavirus" --format fna --source genbank --out-dir betacoronaviruses/

# Download all Complete viral assemblies from RefSeq
gdl --tax-name "Viruses" --format fna --source refseq --assembly-level "Complete Genome"

Installation

Homebrew

brew install audy/tap/gdl

From binary

Binaries are built for macOS, Windows and Linux and are available here

From Source

git clone ...
cargo build --release
(sudo) cp target/release/gdl /usr/local/bin/

Options

--help

Print help and exit.

--tax-id <TAX_ID> / --tax-name <TAX_NAME>

Download all assemblies within the provided taxonomic node.

--no-children

Do not download assemblies assigned to tax IDs below the provided taxonoic node.

--parallel <PARALLEL>

Download concurrently in <PARALLEL> threads.

--format <FORMAT>

File format to retrieve. The default is fna. The possible values are:

• fna - fasta nucleotide, genomic
• faa - fasta amino acid, coding
• gbk - assembly and annotations, genbank format
• gff - assembly and annotations, genomic file format

--out-dir <OUT_DIR>

Output directory to store files in. By default, will use $pwd. If provided, the directly must exist prior to running.

--source <SOURCE>

The source from which to retrieve the genomes. Can be either "refseq" or "genbank" (default=refseq).

--assembly-level <ASSEMBLY_LEVEL>

Filter to only assemblies that match <ASSEMBLY_LEVEL>. Default is to include assemblies with any assembly level value. Possible values are Contig, Scaffold, Complete Genome and Chromosome. For defintions, see NCBI documentation.