Welcome to ENCODEfetch¶

ENCODEfetch CLI

ENCODEfetch is a command-line tool and Python package for retrieving matched case-control datasets and standardized metadata from the ENCODE Project.

It is designed for genomics workflows where you need to search ENCODE, include matched controls, keep a reproducible manifest, and hand the result to downstream pipelines such as nf-core or Snakemake.

Key features¶

Search ENCODE experiments by assay, target, organism, biosample, perturbation state, related series, status, file type, and assembly.
Fetch specific experiment accessions from a comma-separated list or a text file.
Expand experiment-level possible_controls and normalize file-level controlled_by links.
Download files in parallel with resumable transfers, retries, chunk-size control, and Rich progress bars.
Write standardized manifest.tsv and metadata.jsonl outputs for auditing and reuse.
Collapse paired-end FASTQs into fastq_1 and fastq_2 columns.
Generate samplesheets for nf-core and Snakemake workflows.
Use the same search and export functionality from Python scripts and notebooks.

Typical workflow¶

encodefetch \
  --assay-title "TF ChIP-seq" \
  --target-label BRD4 \
  --organism "Homo sapiens" \
  --file-type fastq \
  --status released \
  --metadata-only \
  --nfcore \
  --snakemake

This writes metadata and pipeline samplesheets without downloading FASTQs. Remove --metadata-only when you are ready to download files.

Documentation map¶

Installation: install from PyPI or source.
Quickstart: first complete CLI and Python examples.
Command Line: all user-facing options and common command patterns.
Python API: public functions, return values, and notebook use.
Exporters: nf-core, Nextflow/nf-core, Snakemake, and control strategies.
Outputs: manifest, metadata, downloaded files, and samplesheet columns.