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Determine the search strategy:\n   - If given a bare accession (SRR\u002FSRX\u002FSRS\u002FSRP\u002FPRJNA\u002FSAMN), map it to the correct NCBI database:\n     - `SRR`, `SRX`, `SRS`, `SRP` → `sra`\n     - `PRJNA` → `bioproject`, then link to `sra`\n     - `SAMN` → `biosample`, then link to `sra`\n   - If given a free-text query, use `esearch -db sra` with structured field tags when helpful:\n     - organism: `[Organism]`\n     - library strategy: `[Strategy]`\n     - platform: `[Platform]`\n     - layout: `[Layout]`\n2. Run `esearch -db sra -query \"\u003Cterm>\"` to retrieve UIDs.\n3. Pipe to `esummary -db sra -format json` or `efetch -db sra -format runinfo` for metadata.\n4. For BioProject-level queries, use `esearch -db bioproject | elink -target sra | efetch -format runinfo` to get the full run table.\n5. Parse the run info CSV or JSON to extract: `Run`, `SampleName`, `BioSample`, `Experiment`, `LibraryStrategy`, `LibraryLayout`, `Platform`, `spots`, `bases`, `size_MB`, `PublishDate`.\n6. Report a summary table of matching runs and key metadata.\n7. If the user wants to download, provide the `prefetch` or `fasterq-dump` command with the accession list.\n\n## Output Contract\n\n- Search query used (exact E-utilities command)\n- Number of hits found\n- Summary table with columns: Run (SRR), Sample, BioProject, Strategy, Platform, Layout, Spots, Bases, Size (MB), Date\n- Full accession list suitable for use with `prefetch` or `fasterq-dump`\n- Saved output files when an output directory is provided:\n  - `esearch.json`\n  - `runinfo.csv` (when `efetch -format runinfo` is used)\n  - `accessions.txt` (one SRR per line)\n\n## Limits\n\n- This skill depends on live access to `https:\u002F\u002Feutils.ncbi.nlm.nih.gov\u002Fentrez\u002Feutils\u002F`.\n- NCBI rate limit: 3 requests\u002Fsecond without API key, 10\u002Fsecond with API key. Always pass `--email` for repeated queries.\n- `esummary` JSON field names for SRA differ from the `runinfo` CSV columns; prefer `efetch -format runinfo` for tabular metadata.\n- Private or access-controlled SRA datasets (dbGaP) cannot be retrieved without an authorized token.\n- Very large BioProjects (>10 000 runs) require paging with `WebEnv` + `query_key`.\n- Common failure cases:\n  - confusing SRA database UIDs with run accessions (they are not the same)\n  - querying `bioproject` instead of `sra` when an SRR is needed\n  - omitting `[Organism]` field tag, causing organism name to match free text in other fields\n  - requesting `retmax` > 10 000 without using history server\n","# Skill: Search SRA\n\n## Use When\n\n- A user wants to find sequencing runs, experiments, studies, or biosamples in the NCBI Sequence Read Archive.\n- A user needs to look up SRA accessions (SRR, SRX, SRS, SRP, SAMN) or search by organism, tissue, assay type, or keyword.\n- A user wants to retrieve run metadata (file size, read count, platform, library strategy) before downloading.\n- A user wants to list all runs belonging to a BioProject or BioSample.\n- A user needs to build a manifest of SRR accessions for downstream download with `prefetch` or `fasterq-dump`.\n- A user wants to filter SRA by sequencing platform (Illumina, PacBio, Nanopore) or library layout (PAIRED, SINGLE).\n\n## Inputs\n\n- Required:\n  - one of: free-text search query, SRA\u002FBioProject\u002FBioSample accession, organism name, or NCBI taxonomy ID\n- Optional:\n  - target SRA entity type: `run`, `experiment`, `sample`, `study` (default: `run`)\n  - organism filter (e.g., `\"Homo sapiens\"`, `\"Mus musculus\"`)\n  - library strategy filter (e.g., `RNA-Seq`, `WGS`, `ChIP-Seq`, `ATAC-seq`)\n  - platform filter (e.g., `ILLUMINA`, `PACBIO_SMRT`, `OXFORD_NANOPORE`)\n  - library layout: `PAIRED` or `SINGLE`\n  - date range: `mindate` \u002F `maxdate` in `YYYY\u002FMM\u002FDD`\n  - maximum results to return (`retmax`, default 20)\n  - output format: `json`, `xml`, or `runinfo` CSV\n  - output directory\n\n## Workflow\n\n1. Determine the search strategy:\n   - If given a bare accession (SRR\u002FSRX\u002FSRS\u002FSRP\u002FPRJNA\u002FSAMN), map it to the correct NCBI database:\n     - `SRR`, `SRX`, `SRS`, `SRP` → `sra`\n     - `PRJNA` → `bioproject`, then link to `sra`\n     - `SAMN` → `biosample`, then link to `sra`\n   - If given a free-text query, use `esearch -db sra` with structured field tags when helpful:\n     - organism: `[Organism]`\n     - library strategy: `[Strategy]`\n     - platform: `[Platform]`\n     - layout: `[Layout]`\n2. Run `esearch -db sra -query \"\u003Cterm>\"` to retrieve UIDs.\n3. Pipe to `esummary -db sra -format json` or `efetch -db sra -format runinfo` for metadata.\n4. For BioProject-level queries, use `esearch -db bioproject | elink -target sra | efetch -format runinfo` to get the full run table.\n5. Parse the run info CSV or JSON to extract: `Run`, `SampleName`, `BioSample`, `Experiment`, `LibraryStrategy`, `LibraryLayout`, `Platform`, `spots`, `bases`, `size_MB`, `PublishDate`.\n6. Report a summary table of matching runs and key metadata.\n7. If the user wants to download, provide the `prefetch` or `fasterq-dump` command with the accession list.\n\n## Output Contract\n\n- Search query used (exact E-utilities command)\n- Number of hits found\n- Summary table with columns: Run (SRR), Sample, BioProject, Strategy, Platform, Layout, Spots, Bases, Size (MB), Date\n- Full accession list suitable for use with `prefetch` or `fasterq-dump`\n- Saved output files when an output directory is provided:\n  - `esearch.json`\n  - `runinfo.csv` (when `efetch -format runinfo` is used)\n  - `accessions.txt` (one SRR per line)\n\n## Limits\n\n- This skill depends on live access to `https:\u002F\u002Feutils.ncbi.nlm.nih.gov\u002Fentrez\u002Feutils\u002F`.\n- NCBI rate limit: 3 requests\u002Fsecond without API key, 10\u002Fsecond with API key. 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