Whole-Plasmid Sequencing Check — Consensus vs Your Design
Drop the results your sequencing service sent and the map it should be — every sample of the order checked at once.
Whole-plasmid nanopore sequencing returns one assembled circular consensus, and then the work starts: the assembler began the circle wherever it landed, half the time it hands back the reverse complement, and a 1 bp indel inside a run of six A's is both the commonest basecalling artefact and exactly what a real frameshift looks like. This tool does those three. Drop your map (the SnapGene .dna or GenBank file it lives in) and the results your provider sent — the whole results .zip of an order, or one consensus FASTA — and every sample is compared at once: it works out the rotation and the strand, reports each difference at its position in YOUR numbering, and says which identical-base run each indel sits in. Differences in the two contexts providers document as nanopore error modes — a homopolymer longer than 9, or a Dam (GATC) / Dcm (CCWGG) methylation site — are marked so you confirm them before acting, and a consensus that came back as a dimer or trimer of your plasmid is recognised and compared one copy at a time. An annotated map reads every difference against its features — silent, missense with the codon number, or a premature stop.
0 bp. An annotated record is what turns a position into “silent in AmpR” or “a stop at codon 41”.
0 bp
How to use the Whole-Plasmid Sequencing Check tool
- 1Drop your design — the SnapGene .dna or GenBank map, which is what turns a position into a consequence — or paste it.
- 2Drop the results .zip your sequencing service sent (or one consensus FASTA / GenBank); an order of several samples becomes a table with one verdict per sample.
- 3Read the verdict, then the difference table: each row carries the change, the feature it lands in, and the homopolymer run if it is in one.
Frequently asked questions
My consensus and my map do not start at the same base. Does that matter?
No. An assembler starts the circle wherever its algorithm landed, so the two almost never line up as written — end to end as linear strings they look about 0% identical. The rotation is found for you, and the result says how far it was and whether the consensus also had to be reverse-complemented.
Is a 1 bp indel a real mutation or a sequencing error?
Nothing in a sequence decides that, so this does not claim to. What it does is tell you when the indel sits inside a run of identical bases, because that is where long-read basecallers miscount and also where real slippage happens. It is the signal to go back to the reads, not a verdict either way.
Which differences should I confirm by Sanger before trusting them?
The ones marked as a known nanopore error context. Whole-plasmid providers document two error modes for nanopore consensus — methylation sites and homopolymers longer than 9 — and only mark them inside their own reports. Every difference sitting in a homopolymer of 10 or more, or on an E. coli Dam (GATC) or Dcm (CCWGG) methylation site, is flagged here wherever the results came from, so you know which ones to re-check with a Sanger read before re-ordering or discarding a clone.
What does this NOT check?
How much of the plasmid the sequencing actually covered, and whether the prep was homogeneous. A consensus is reported at full length whatever the coverage behind it was, and a mixed population collapses to one sequence before this tool sees it. If you have the reads, sequencing_readback_verify answers both.