Skill: Search GSA

Use When

A user wants to find sequencing data deposited in the CNCB Genome Sequence Archive (GSA) at ngdc.cncb.ac.cn.
A user needs to look up GSA accessions: CRA (project), CRX (experiment), CRR (run), CRS (sample), or SAMC (biosample).
A user wants to retrieve run-level metadata (read count, file size, platform, library strategy) for data in GSA.
A user wants to search GSA by organism, tissue, disease, keyword, or data type.
A user wants to list all runs belonging to a GSA project (CRA accession).
A user needs the download URL or FASP path for CRR files from CNCB.

Required:
- one of: free-text search query, GSA accession (CRA/CRX/CRR/CRS/SAMC), organism name, or NCBI taxonomy ID
Optional:
- data type filter: Genome, Transcriptome, Metagenome, Epigenome, Variation, Proteome
- library strategy filter (e.g., RNA-Seq, WGS, ChIP-Seq, ATAC-Seq)
- sequencing platform (e.g., Illumina, PacBio, ONT)
- organism filter (scientific name or taxonomy ID)
- output format: json or tsv
- maximum results (size, default 20)
- output directory

Determine the access method:
- Direct accession lookup: construct the CNCB accession detail URL:
  - https://ngdc.cncb.ac.cn/gsa/browse/<CRA-accession> for projects
  - https://ngdc.cncb.ac.cn/gsa/run/<CRR-accession> for individual runs
- Keyword search: use the GSA search API endpoint:
```
GET https://ngdc.cncb.ac.cn/gsa/search?searchTerm=<query>&page=1&pageSize=20
```
- Programmatic metadata fetch: use the GSA data API:
```
GET https://ngdc.cncb.ac.cn/gsa/api/v1/project/<CRA>
GET https://ngdc.cncb.ac.cn/gsa/api/v1/run/<CRR>
```
Parse the response to extract: accession, title, organism, submission date, run count, total bases, platform, and library strategy.
For project-level queries, enumerate all CRR runs and collect per-run metadata.
Construct download URLs for CRR files:
- FTP: ftp://download.cncb.ac.cn/gsa/<CRA>/<CRX>/<CRR>/
- HTTPS: https://download.cncb.ac.cn/gsa/<CRA>/<CRX>/<CRR>/
Report a summary table and the accession list.

Search or fetch request URL used
Number of matching projects or runs
Summary table with columns: Accession (CRR/CRA), Title, Organism, Platform, Strategy, Spots, Bases, Size, Submission Date
Download URL(s) for CRR files
Accession list saved to accessions.txt when an output directory is provided
Optional metadata.json or metadata.tsv with full per-run fields

GSA web API is subject to change; confirm endpoint availability with a test request if needed.
Some datasets in GSA are access-controlled and require registration at ngdc.cncb.ac.cn before download.
GSA accessions follow CNCB conventions (CRA/CRX/CRR/CRS) distinct from NCBI (SRP/SRX/SRR/SRS); do not mix them.
CNSA (China National Sequence Archive, for assembled genomes) is a separate archive also at CNCB; GSA is specifically for raw sequencing data.
The FTP server may be slow for users outside mainland China; HTTPS is generally preferred.
Common failure cases:
- confusing CRA (project) with CRR (run) accession types
- attempting to use NCBI E-utilities with GSA accessions (they are not indexed by NCBI)
- missing authentication cookie when accessing controlled-access datasets
- constructing download paths without the correct CRA/CRX/CRR hierarchy