{
  "id": "sratoolkit",
  "name": "SRA Toolkit",
  "homepage": "https://github.com/ncbi/sra-tools",
  "description": "A toolkit for using data in the INSDC Sequence Read Archives.",
  "executables": [
    "prefetch",
    "fasterq-dump",
    "vdb-config"
  ],
  "dotfiles": {
    "paths": [
      "~/.ncbi/user-settings.mkfg"
    ],
    "secret": []
  },
  "commands": {
    "format": 1,
    "label": "Download SRA accessions (prefetch)",
    "description": "Download one or more SRA run accessions with prefetch, resumable on failure. Only prefetch is covered; fasterq-dump and vdb-config have no form.",
    "quality": "ai-draft",
    "parser": {
      "end_of_options": "--",
      "interleave": "permute",
      "long_equals": true,
      "short_attached": true,
      "short_bundles": false
    },
    "source": [
      {
        "id": "wiki",
        "kind": "manual",
        "url": "https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump",
        "revision": "2026-10-27",
        "evidence": "$prefetch SRR000001 -O /path/to/be/used\nMake sure the last directory of /path/to/be/used is the accession itself.\n$prefetch SRR1951777 --max-size 420000000000\nkilobytes (default): --max-size 10 == --max-size 10k : 10 kilobytes,\nmegabytes: --max-size 10m : 10 megabytes,\ngigabytes: --max-size 10g : 10 gigabytes,\nterabytes: --max-size 10t : 10 terabytes,\nunlimited: --max-size u.\nIf prefetch fails - run the same prefetch command again and the download will resume.\n"
      }
    ],
    "field": [
      {
        "id": "accessions",
        "label": "Accessions",
        "description": "SRA run accessions such as SRR000001.",
        "type": "string",
        "position": 0,
        "min": 1,
        "multiple": true,
        "sources": [
          "wiki"
        ]
      },
      {
        "id": "output_dir",
        "label": "Output directory",
        "description": "The last directory should be named after the accession.",
        "type": "path",
        "option": [
          "-O"
        ],
        "path": {
          "kind": "directory",
          "role": "output"
        },
        "sources": [
          "wiki"
        ]
      },
      {
        "id": "max_size",
        "label": "Maximum download size",
        "description": "Default limit is 20G. Suffixes k, m, g, t; u means unlimited.",
        "type": "string",
        "option": [
          "--max-size"
        ],
        "suggestions": [
          {
            "value": "u",
            "label": "Unlimited"
          },
          {
            "value": "100g",
            "label": "100 GB"
          }
        ],
        "sources": [
          "wiki"
        ]
      }
    ],
    "task": [
      {
        "id": "download",
        "label": "Download accessions",
        "fields": [
          "accessions",
          "output_dir"
        ],
        "required": [
          "accessions"
        ]
      },
      {
        "id": "large",
        "label": "Download a large accession",
        "fields": [
          "accessions",
          "max_size",
          "output_dir"
        ],
        "required": [
          "accessions",
          "max_size"
        ],
        "set": {
          "max_size": [
            "u"
          ]
        }
      }
    ],
    "group": [
      {
        "id": "basic",
        "label": "Basic",
        "fields": [
          "accessions",
          "output_dir"
        ]
      },
      {
        "id": "advanced",
        "label": "Advanced",
        "fields": [
          "max_size"
        ]
      }
    ]
  }
}