Files & formats

Sanger de novo assembly

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.

post/sanger_assemble

Request

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

Request body

readsobject[]

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.

fastastring

Alternative to reads: a multi-record FASTA of the reads. No quality, so no end trimming.

minOverlapinteger

Shortest overlap that may join two reads.

minIdentitynumber

Lowest percent identity an overlap may have.

trimThresholdnumber

Phred threshold for end-trimming. Ignored for reads with no quality array.

noTrimboolean

Assemble the reads exactly as given, with no quality trimming.

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.