---
title: "Sanger de novo assembly"
method: POST
path: "/sanger_assemble"
tags: ["Files & formats"]
---

# Sanger de novo assembly

`POST /sanger_assemble`

## Request

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

Assemble two or more Sanger reads into a contig WITHOUT a reference sequence — the forward/reverse pair of one insert, or a set of tiling reads. Orientation is worked out from the overlaps, ends are quality-trimmed, and the consensus is quality-weighted. Reports depth and agreement per position, every position where the reads disagree (including a base only one read has), and any read that overlapped nothing. Use sanger_vs_reference instead when you already know what the sequence should be.

## Request body

- object
  - `reads` object[]: The reads, as [{name, sequence, quality?}]. `quality` is a per-base Phred array the same length as `sequence`; without it the read still assembles but its ends are NOT trimmed, which the result says.
  - `fasta` string: Alternative to `reads`: a multi-record FASTA of the reads. No quality, so no end trimming.
  - `minOverlap` integer: Shortest overlap that may join two reads.
  - `minIdentity` number: Lowest percent identity an overlap may have.
  - `trimThreshold` number: Phred threshold for end-trimming. Ignored for reads with no quality array.
  - `noTrim` boolean: Assemble the reads exactly as given, with no quality trimming.

## 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)