{
  "id": "blast",
  "name": "BLAST+",
  "homepage": "https://blast.ncbi.nlm.nih.gov/",
  "description": "Basic Local Alignment Search Tool",
  "executables": [
    "blastn",
    "blastp",
    "blastx",
    "tblastn",
    "tblastx",
    "makeblastdb"
  ],
  "dotfiles": {
    "paths": [
      "~/.ncbirc"
    ],
    "secret": []
  },
  "commands": {
    "format": 1,
    "label": "BLAST+ blastn",
    "description": "Search a nucleotide query file against a BLAST database with blastn. Only the flags shown in NCBI's BLAST+ documentation examples are offered; the other BLAST+ programs and tuning options are left out.",
    "quality": "ai-draft",
    "parser": {
      "end_of_options": "--",
      "interleave": "permute",
      "long_equals": false,
      "short_attached": false,
      "short_bundles": false
    },
    "source": [
      {
        "id": "docs",
        "kind": "help",
        "url": "https://raw.githubusercontent.com/ncbi/blast_plus_docs/master/README.md",
        "revision": "2026-10-27",
        "evidence": "blastn -query /blast/queries/query1.fa -db nt -num_threads 16 \\\n-out /blast/results/blastn.query1.denovo16s.out\nPlease note that running the `blastn` binary without specifying its `-task` parameter invokes the MegaBLAST algorithm.\n"
      }
    ],
    "field": [
      {
        "id": "query",
        "label": "Query file",
        "type": "path",
        "option": [
          "-query"
        ],
        "path": {
          "kind": "file",
          "role": "input",
          "must_exist": true
        },
        "sources": [
          "docs"
        ]
      },
      {
        "id": "db",
        "label": "Database",
        "description": "BLAST database name, for example nt.",
        "type": "string",
        "option": [
          "-db"
        ],
        "sources": [
          "docs"
        ]
      },
      {
        "id": "out",
        "label": "Output file",
        "type": "path",
        "option": [
          "-out"
        ],
        "path": {
          "kind": "file",
          "role": "output"
        },
        "effect": "overwrite",
        "sources": [
          "docs"
        ]
      },
      {
        "id": "num_threads",
        "label": "Threads",
        "type": "integer",
        "option": [
          "-num_threads"
        ],
        "sources": [
          "docs"
        ]
      },
      {
        "id": "task",
        "label": "Task",
        "description": "Without -task, blastn runs the MegaBLAST algorithm.",
        "type": "string",
        "option": [
          "-task"
        ],
        "sources": [
          "docs"
        ]
      }
    ],
    "task": [
      {
        "id": "search",
        "label": "Search a database",
        "fields": [
          "query",
          "db",
          "out",
          "num_threads",
          "task"
        ],
        "required": [
          "query",
          "db"
        ]
      }
    ],
    "group": [
      {
        "id": "basic",
        "label": "Basic",
        "fields": [
          "query",
          "db",
          "out",
          "num_threads",
          "task"
        ]
      }
    ]
  }
}