search-datasets

name	search-datasets
description	Find sequencing datasets (NCBI SRA / EMBL-EBI ENA runs) by phenotype or disease, focused on aligned BAM/CRAM reads. Use when the user wants to locate sequencing data, aligned reads, BAM/CRAM files, FASTQ runs, or datasets for a disease, phenotype, or MONDO id.
when_to_use	Trigger on requests like "find aligned reads for ataxia", "what SRA/ENA datasets exist for <disease>", "find BAM/CRAM files for <phenotype>", "search sequencing runs for <MONDO id>", or "WGS/exome datasets for <disease>".
allowed-tools	Bash(aligned-read-search *) Bash(python -m aligned_read_search *) Bash(pip install *) Bash(pip show *) Bash(command -v *)

Find sequencing datasets by phenotype

This skill drives the aligned-read-search CLI, which searches NCBI SRA and EMBL-EBI ENA for sequencing runs matching a phenotype/disease and flags which runs have an aligned BAM/CRAM file. It expands the phenotype to synonyms and disease subtypes via the MONDO ontology, so a generic term like "ataxia" also finds its subtypes.

Step 1 — Ensure the tool is installed

Check whether the CLI is available:

command -v aligned-read-search

If that prints nothing, install the package. Prefer the copy bundled with this plugin when available ($CLAUDE_PLUGIN_ROOT), otherwise install from GitHub:

pip install -e "${CLAUDE_PLUGIN_ROOT}" 2>/dev/null \
  || pip install "git+https://github.com/broadinstitute/SequencingReadDataSearch.git"

If a later command fails with numpy.core.multiarray failed to import or _ARRAY_API not found, the environment has NumPy 2.x but pandas/pyarrow were built against 1.x. Fix it and retry:

pip install 'numpy<2'

Step 2 — Run the search

Always pass --json so the output is machine-readable:

aligned-read-search "<phenotype>" --json

Useful flags (short / long):

• -a, --archive ena,sra — which archives to query (default: both).
• -l, --limit N — max results per archive (default: 50).
• -e, --exact — literal match; skip MONDO ontology expansion.
• -u, --include-unaligned — also include runs without a BAM/CRAM file.
• -s, --library-strategy WGS,WXS — filter by strategy (e.g. WGS, WXS, RNA-Seq).
• -v, --verbose — print progress to stderr (handy when a query is slow).

Important defaults and tips:

• By default only runs with an aligned BAM/CRAM file are returned. Pass -u/--include-unaligned to see everything.
• Aligned files are sparse for many phenotypes. If the result is empty, retry with a larger limit (e.g. -l 500) before concluding there is nothing.
• A MONDO id works in place of a name, e.g. aligned-read-search MONDO:0100254.

Step 3 — Report results

Parse the JSON and summarize for the user:

• How many runs matched, and how many have alignment files.
• For aligned runs, list run_accession, library_strategy, organism, the matched phenotype_match tokens, and the alignment_urls (BAM/CRAM download links).
• Surface read_urls (FASTQ) when the user wants the raw reads.

Example:

aligned-read-search ataxia -a ena -l 200 --json