Files & formats

Why is this Sanger read bad?

Diagnose a failing Sanger chromatogram: the longest usable window (Mott trimming), whether there is signal above the noise at all, whether more than one molecule is in the tube and from which base, whether quality collapsed at a homopolymer or tandem repeat the polymerase stuttered through, and whether a dye blob or the instrument's own separation is the problem rather than the DNA. Each finding carries the measurement it is based on, what that pattern is usually caused by, and what to do next. Reads .ab1, .abi and .scf.

post/trace_diagnose

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/trace_diagnose
  • Auth: none required

Request body

fileBase64string required

The binary trace file (.ab1 / .abi / .scf), base64-encoded.

fileNamestring

Optional original file name (echoed back, and used to explain a refusal).

qualityCutoffnumber

Phred score the usable window is measured at. 20 is the conventional 1-in-100 line.

mixedRationumber

A second peak at or above this fraction of the called peak counts as a mixed position. Lower it to catch a minor species, raise it if ordinary crosstalk on your instrument is firing it.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.