Genomes

Assembly listings with BUSCO metrics, detail views with gene lists, chromosomes, and quality diagnostics.

`GET /api/v1/genomes`

Paginated list of genome assemblies with sorting, filtering, and faceted navigation.

curl "https://api.ilepbase.com/api/v1/genomes?page=1&pageSize=10&sortBy=buscoCompletePct&sortDirection=desc"

Query Parameters

Name	Type	Required	Default	Description
`q`	`string`	No	—	Full-text search across species, family, genus.
`page`	`int`	No	`1`	Page number.
`pageSize`	`int`	No	`10`	Items per page.
`sortBy`	`string`	No	—	Sort field: `insectSpecies`, `family`, `subfamily`, `genus`, `sizeMb`, `n50Kb`, `buscoCompletePct`, `source`.
`sortDirection`	`string`	No	`desc`	`asc` or `desc`.
`family`	`string`	No	—	Filter by family name.
`subfamily`	`string`	No	—	Filter by subfamily name.
`source`	`string`	No	—	Data source filter, such as `NCBI`.

Response

{
  "success": true,
  "data": {
    "items": [
      {
        "id": "papilio-xuthus",
        "insectSpecies": "Papilio xuthus",
        "commonName": "柑橘凤蝶",
        "family": "Papilionidae",
        "subfamily": "Papilioninae",
        "genus": "Papilio",
        "sizeMb": 257,
        "n50Kb": 1240,
        "buscoCompletePct": 95.2,
        "source": "NCBI",
        "sourceUrl": "https://www.ncbi.nlm.nih.gov/assembly/GCA_000836235.1",
        "downloadUrl": "/downloads/papilio-xuthus-genome.fa.gz",
        "assemblyAccession": "GCA_000836235.1",
        "assemblyLevel": "chromosome",
        "hasBrowser": true
      }
    ],
    "pagination": {
      "page": 1, "pageSize": 10,
      "total": 48, "totalPages": 5,
      "hasNext": true, "hasPrev": false
    },
    "query": {
      "q": "",
      "page": 1, "pageSize": 10,
      "sortBy": "buscoCompletePct",
      "sortDirection": "desc",
      "family": null, "subfamily": null, "source": null,
      "hasBrowser": null
    },
    "facets": {
      "families": [
        { "value": "Papilionidae", "count": 12 },
        { "value": "Noctuidae", "count": 10 }
      ],
      "subfamilies": [ ... ],
      "sources": [
        { "value": "NCBI", "count": 35 },
        { "value": "GCA", "count": 13 }
      ]
    }
  },
  "timestamp": "2026-04-23T12:00:00.000Z"
}

Key Fields

Field	Type	Description
`items[].insectSpecies`	`string`	Scientific name.
`items[].sizeMb`	`number`	Genome assembly size in megabases.
`items[].n50Kb`	`number`	Scaffold N50 in kilobases.
`items[].buscoCompletePct`	`number`	BUSCO completeness percentage.
`items[].assemblyLevel`	`string`	Assembly level: `chromosome`, `scaffold`, `contig`.
`items[].hasBrowser`	`boolean`	Whether a JBrowse genome browser is available.

`GET /api/v1/genomes/{id}`

Full genome detail: assembly statistics, BUSCO quality diagnostics, gene list, chromosome ideogram data, download file manifest, and linked publications.

curl https://api.ilepbase.com/api/v1/genomes/papilio-xuthus

Response (abridged)

{
  "success": true,
  "data": {
    "id": "papilio-xuthus",
    "family": "Papilionidae",
    "subfamily": "Papilioninae",
    "insectSpecies": "Papilio xuthus",
    "genus": "Papilio",
    "commonName": "柑橘凤蝶",
    "n50": "1.2 Mb",
    "busco": "95.2%",
    "assembly": {
      "accession": "GCA_000836235.1",
      "assemblyLevel": "chromosome",
      "genomeSizeMb": 257,
      "scaffoldCount": 210,
      "contigCount": 1845,
      "gcContent": 35.8,
      "chromosomeCount": 30,
      "scaffoldN50": "12.4 Mb",
      "contigN50": "1.2 Mb",
      "totalGapLengthMb": 12.3,
      "annotationMethod": "BRAKER2",
      "submitter": "iLepBase Consortium",
      "submissionDate": "2024-03-15"
    },
    "quality": {
      "summary": "BUSCO v5.4.4, Lepidoptera_odb10 (1690 markers)",
      "complete": { "percentage": 95.2, "count": 1608 },
      "singleCopy": { "percentage": 94.1, "count": 1590 },
      "duplicated": { "percentage": 1.1, "count": 18 },
      "fragmented": { "percentage": 1.8, "count": 30 },
      "missing": { "percentage": 3.0, "count": 50 },
      "markers": 1690,
      "lineageDataset": "Lepidoptera_odb10",
      "buscoVersion": "5.4.4",
      "mode": "genome",
      "genePredictor": "Augustus"
    },
    "genes": [
      {
        "geneId": "PXUT_00001",
        "symbol": "COI",
        "chromosome": "1",
        "start": 123456,
        "end": 125000,
        "strand": "+",
        "description": "Cytochrome c oxidase subunit I"
      }
    ],
    "chromosomes": [
      {
        "name": "1",
        "refName": "NC_045100.1",
        "length": 15234567,
        "gcContent": 35.2,
        "sortOrder": 1
      }
    ],
    "browser": {
      "datasetLabel": "Papilio xuthus genome",
      "assemblyName": "Pxut_1.0",
      "refName": "NC_045100.1",
      "regionStart": 1,
      "regionEnd": 15234567,
      "defaultLocation": "NC_045100.1:1..50000"
    },
    "downloads": [
      { "label": "Assembly (FASTA)", "format": "fasta.gz", "size": "87 MB", "href": "..." },
      { "label": "Annotation (GFF3)", "format": "gff3.gz", "size": "12 MB", "href": "..." },
      { "label": "Protein (FAA)", "format": "faa.gz", "size": "5 MB", "href": "..." }
    ],
    "publications": [
      {
        "title": "Chromosome-level genome assembly of Papilio xuthus",
        "authors": "Li J, Zhang A, et al.",
        "journal": "GigaScience",
        "year": 2024,
        "pubmedHref": "https://pubmed.ncbi.nlm.nih.gov/...",
        "doiHref": "https://doi.org/10.1093/..."
      }
    ]
  },
  "timestamp": "2026-04-23T12:00:00.000Z"
}

Genomes

GET /api/v1/genomes

GET /api/v1/genomes/{id}

On this page

`GET /api/v1/genomes`

`GET /api/v1/genomes/{id}`