---
title: "Whole-plasmid sequencing: consensus vs design"
method: POST
path: "/whole_plasmid_verify"
tags: ["Files & formats"]
---

# Whole-plasmid sequencing: consensus vs design

`POST /whole_plasmid_verify`

## Request

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

Compare a whole-plasmid sequencing CONSENSUS (the single circular FASTA a nanopore plasmid service returns) against the design it was supposed to be, and say whether they are the same molecule. Finds the rotation and strand itself — an assembler starts the circle wherever it landed and half the time returns the reverse complement, so the two almost never line up as written — then reports every difference in the DESIGN's own coordinates. Each difference carries the length of the identical-base run it sits in, because a 1 bp indel inside a homopolymer is both the commonest long-read basecalling artefact and what a real slippage mutation looks like, and a bare difference list cannot tell them apart. Pass the design as an annotated GenBank record and every difference is also read against its features: silent, missense with the codon number, or a premature stop. Complements sequencing_readback_verify, which aligns raw READS through minimap2; this one needs no reads and no sidecar.

Batchable via `POST /batch`.

## Request body

- object
  - `design` string, required: What you meant to build: raw bases, FASTA, or your annotated GenBank record. An annotated record is what turns a position into a consequence.
  - `consensus` string, required: The assembled consensus from the sequencing service, raw or FASTA. One record.
  - `circular` boolean: Treat both as circular (the default, and right for a plasmid). The consensus is then rotated and, if needed, reverse-complemented into the design's frame before anything is compared. Turn it off only for a linear product, where the ends are meaningful.

## 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)