---
title: "Assembly outcomes (what else you might have built)"
method: POST
path: "/assembly_outcomes"
tags: ["Enzymes & cloning"]
---

# Assembly outcomes (what else you might have built)

`POST /assembly_outcomes`

## Request

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

Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two parts swapped, the backbone self-circularized — as full sequences, ranked by how few independent mis-ligations each needs. Golden Gate outcomes are annotated with the MEASURED overhang cross-talk they would have to exploit (Potapov/Pryor ligation data). Feed the result to diagnostic_digest to pick a screening enzyme. Reports no probability per outcome: the ligation data does not measure transformation or vector background.

## Request body

- object
  - `fragments` string[], required: The parts in assembly order, raw or FASTA — the same list cloning_simulate takes. 2-8 parts.
  - `names` string[]: Optional labels for the parts, in the same order ("backbone", "promoter", "CDS"). Used in every outcome label.
  - `method` 'goldengate' | 'gibson': How the parts are joined. Golden Gate junctions are the Type IIS fusion overhangs; Gibson junctions are the homology arms.
  - `enzyme` string: Golden Gate only — the Type IIS enzyme, which fixes the overhang length (BsaI, BbsI, Esp3I (BsmBI)).
  - `overlapLen` number: Gibson only — homology arm length, which must match what the assembly was designed with.
  - `dataset` 'generic-t4-37c-1h' | 'bsai-hfv2': Which ligation dataset to read overhang cross-talk from (Golden Gate only).
  - `circular` boolean: Circular product. Only circular assemblies are covered — a linear product's leading end is a free terminus, not a junction.
  - `maxAlternatives` number: Cap on returned alternatives, most accessible first. The pre-cap count is always reported as alternativesEnumerated.

## 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)