Command Line

The console entry point is available as both encodefetch and ENCODEfetch.

encodefetch --help

Search by filters

encodefetch \
  --assay-title "Histone ChIP-seq" \
  --target-label H3K27ac \
  --organism "Mus musculus" \
  --file-type bam \
  --status released \
  --metadata-only \
  --threads 8

Search by accession

encodefetch \
  --accessions ENCSR514EOE,ENCSR395MHA \
  --file-type fastq \
  --metadata-only \
  --nfcore

Options

Option	Purpose
--accessions	Comma-separated experiment accessions, or a text file with one accession per line.
--assay-title	ENCODE assay title, such as TF ChIP-seq, Histone ChIP-seq, ATAC-seq, or RNA-seq.
--target-label	Target label. Repeat the option for multiple targets.
--organism	Organism scientific name, for example Homo sapiens or Mus musculus.
--biosample	Biosample ontology term name.
--file-type	File formats to include: fastq, bam, bed, bigWig, tsv, bw, or bedpe.
--assembly	Genome assembly filter for non-FASTQ files.
--status	File status filter. Defaults to released.
--perturbed	Filter experiments by perturbation state with true or false.
--series	Filter experiments by related ENCODE series @type, such as OrganismDevelopmentSeries.
--outdir	Output directory. Defaults to encode_results.
--metadata-only	Write metadata and samplesheets only; skip downloads.
--threads	Worker count for metadata fetching, control fetching, and downloads.
--max-retries	Maximum HTTP retries per file during download.
--chunk-size	Download chunk size in bytes.
--auth-token	ENCODE API token.
--progress / --no-progress	Enable or disable progress bars.
--nfcore	Write an nf-core samplesheet for the selected assay.
--snakemake	Write a Snakemake samplesheet for the selected assay.
--control-strategy	Choose all, pool, best, or first for multiple controls in samplesheets.
--dry-run	Deprecated alias for --metadata-only.
--version	Show the installed version.

Notes

The manifest always preserves all matched controls in matched_control_experiments. When ENCODE provides file-level control relationships, ENCODEfetch stores normalized control file accessions in controlled_by_files.

--control-strategy changes only samplesheet output:

• all: write one case row per resolved control.
• pool: write one case row with controls joined by semicolons.
• first: write one case row with the first resolved control.
• best: write one case row with the highest-scoring control based on biosample, organism, lab, replicate, file, and release metadata.

See Exporters for the full ranking details.