{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://schema.humancellatlas.org/type/file/9.6.0/sequence_file",
  "description": "A file of read sequences generated by a sequencing experiment.",
  "additionalProperties": false,
  "required": [
    "describedBy",
    "schema_type",
    "file_core",
    "read_index"
  ],
  "title": "Sequence file",
  "name": "sequence_file",
  "type": "object",
  "properties": {
    "describedBy": {
      "description": "The URL reference to the schema.",
      "type": "string",
      "pattern": "^(http|https)://schema.(.*?)humancellatlas.org/type/file/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/sequence_file"
    },
    "schema_version": {
      "description": "The version number of the schema in major.minor.patch format.",
      "type": "string",
      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
      "example": "4.6.1"
    },
    "schema_type": {
      "description": "The type of the metadata schema entity.",
      "type": "string",
      "enum": [
        "file"
      ]
    },
    "provenance": {
      "description": "Provenance information provided by the system.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/system/1.1.0/provenance"
    },
    "file_core": {
      "description": "Core file-level information.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/core/file/6.4.0/file_core",
      "user_friendly": "File core"
    },
    "read_index": {
      "description": "The sequencing read this file represents.",
      "type": "string",
      "example": "Should be one of: read1, read2, index1, index2",
      "enum": [
        "read1",
        "read2",
        "read3",
        "read4",
        "index1",
        "index2",
        "single-end, non-indexed"
      ],
      "user_friendly": "Read index",
      "guidelines": "If a sequencing experiment is single-end, enter 'read1'."
    },
    "lane_index": {
      "description": "The lane that this file was sequenced from.",
      "type": "integer",
      "example": 1,
      "user_friendly": "Lane index"
    },
    "read_length": {
      "description": "The length of a sequenced read in this file, in nucleotides.",
      "type": "integer",
      "example": 51,
      "user_friendly": "Read length"
    },
    "insdc_run_accessions": {
      "description": "An International Nucleotide Sequence Database Collaboration (INSDC) run accession.",
      "type": "array",
      "items": {
        "pattern": "^[D|E|S]RR[0-9]+$",
        "type": "string"
      },
      "user_friendly": "INSDC run accession",
      "example": "SRR0000000",
      "guidelines": "Enter accession if run has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with DRR, SRR, or ERR, respectively."
    },
    "sequencing_run_batch": {
      "description": "An identifier that indicates which runs were sequenced in the same batch.",
      "type": "string",
      "user_friendly": "Sequencing run batch",
      "example": "run1; sequencing_batch_37; NV0087"
    },
    "library_prep_id": {
      "description": "A unique ID for the library preparation.",
      "type": "string",
      "example": "tech_rep_group_001",
      "user_friendly": "Library preparation ID",
      "guidelines": "Indicate which samples are from the same library preparation by providing a unique identifier for each library preparation."
    }
  }
}