---
title: "HDR donor designer"
method: POST
path: "/crispr_hdr_donor"
tags: ["CRISPR"]
---

# HDR donor designer

`POST /crispr_hdr_donor`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/crispr_hdr_donor`
- Auth: none required

Build an HDR donor (homology arms flanking an edit) from a target sequence and either an explicit edit window (editStart/editEnd) or a guide's cut site (guideStart/guideEnd/guideStrand/nuclease — SpCas9-family only; Cas12a's staggered cut needs an explicit editStart/editEnd). Also designs genotyping primers spanning the edit site on the original sequence (a real size-shift or sequencing target to confirm the edit), reusing the same primer-design engine as primer_design.

## Request body

- object
  - `targetSequence` string, required: Nucleotide sequence (raw or FASTA; IUPAC accepted).
  - `editStart` integer: 1-based start of the region being replaced. Omit to derive from guideStart/guideEnd/guideStrand instead.
  - `editEnd` integer: 1-based inclusive end of the region being replaced; editEnd = editStart-1 denotes a pure insertion with nothing removed. Omit to derive from the guide's cut site.
  - `guideStart` integer: 1-based forward-strand start of the guide's protospacer (alternative to editStart/editEnd, for an insertion exactly at the cut site).
  - `guideEnd` integer: 1-based forward-strand end of the guide's protospacer.
  - `guideStrand` '+' | '-': Strand the guide's protospacer is on.
  - `nuclease` 'spcas9' | 'spcas9ng' | 'sacas9' | 'cas12a': Needed only when deriving the cut site from guideStart/guideEnd/guideStrand.
  - `replacement` string, required: Sequence to insert/substitute ("" for a pure deletion).
  - `armLength` integer: Homology arm length (bp) on each side. Use ~30–60 for an ssODN donor, ~500–1000 for a dsDNA donor plasmid.
  - `designGenotypingPrimers` boolean: Also design a primer pair (on the original targetSequence) whose product spans the edit site.
  - `blockPam` boolean: When a SpCas9-family guide is supplied and the edit does not already disrupt its PAM, fold a PAM-blocking mutation (silent when a CDS frame is given) into the donor so the edited allele can't be re-cut.
  - `frameStart` integer: Optional 1-based CDS reading-frame start; makes the PAM-blocking mutation synonymous where possible.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)