Primers & oligos

Which sequencing reads actually tell your candidates apart

Given the molecules a cloning reaction could have produced and the sequencing primers you could use, work out which primers separate which pairs of candidates — and return the smallest set that separates every pair any of them can. Scores a read by discrimination, not coverage: a read of 700 bases every candidate shares is worth nothing, and a short read across a junction is worth everything. Names the pairs no primer here separates, so you find out before paying for the reads rather than after. Pair it with outcome_deconvolve once the traces come back.

post/read_placement_plan

Request

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

Request body

candidatesobject[] required

The molecules this reaction could produce, as { id, label, sequence, circular? }. Between 2 and 24; assembly_outcomes' intended plus alternatives is the intended source.

primersobject[] required

Sequencing primers to choose between, as { id, label, sequence }. Up to 32.

usableFromnumber

Bases after the primer's 3' end before the trace becomes readable (0-500). A difference inside this dead zone is not counted as a separation, because the trace cannot show it.

usableLengthnumber

Readable bases per reaction, counted from usableFrom (50-5000).

maxMismatchesinteger

Mismatch budget passed to the priming scan. Defaults to primer-binding's own (~10% of the primer's length).

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.