Files & formats

Whole-plasmid sequencing: consensus vs design

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.

post/whole_plasmid_verify

Request

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

Request body

designstring 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.

consensusstring required

The assembled consensus from the sequencing service, raw or FASTA. One record.

circularboolean

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

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.