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Full PlasmidSeq – Complete Plasmid Sequencing with ONT

Full PlasmidSeq: State-of-the-Art Plasmid Sequencing Service
 
 
Complete plasmid sequences, no primers needed.
Full PlasmidSeq uses Oxford Nanopore long-read sequencing combined with Microsynth’s advanced bioinformatics pipeline. The result is a closed-circle, fully annotated plasmid sequence—fast, accurate, and cost-effective. Available for samples in tubes or 96-well plates.
 

What You Can Achieve

  • Obtain the full plasmid sequence in a single experiment
  • Verify plasmid integrity and detect unwanted mutations
  • Confirm plasmid maps from shared or purchased sources (e.g. Addgene)
  • Resolve cloning issues caused by sequence errors
  • Save time and cost compared to primer-based Sanger sequencing
  • Archive complete plasmid sequences for long-term use

Bioinformatics Analysis

With Full PlasmidSeq you receive a comprehensive results package, including both standard sequence files and intuitive visualizations for easy interpretation:

  • Consensus sequence
    • Final assembled plasmid sequence (.fasta)
    • Annotated plasmid sequence (.gbk)
  • Plasmid map
    • Interactive, browser-ready map (.annotation.html)
    • Publication-ready annotated GenBank file (.annotation.gbk)
  • Quality overview
    • Comprehensive summary report with size, coverage, read depth, and mapping statistics (.overview.html)
    • Read depth plot across the plasmid (.depth.pdf)
  • Raw and supporting data
    • Basecalled reads with quality scores (.fastq)
    • Coverage and quality metrics (.coverage.tsv)
    • Base-by-base mismatch and indel statistics (.mapping.tsv, .uncertain.tsv)
  • Intuitive visualization
    • Sanger-like pseudo-electropherograms (.ab1) for a familiar, easy-to-read view of sequence quality
    • Read length distribution plots included in the interactive report
  • Optional
    • Complete raw reads (*raw.reads.fastq.gz) available on request

Turnaround Time

  • Results within 1–2 working days after sample receipt
  • Results delivered Monday to Friday

Use our Microsynth drop boxes for free and convenient shipment.

How to Order

Procedure to order labels for our Full PlasmidSeq/Long PCRSeq:

  1. Enter our webshop.
  2. Select Tubes or Plates under Full PlasmidSeq / Long PCRSeq.
  3. Choose between prepaid and non-prepaid labels.
  4. Generate labels, prepare samples, and ship.

Procedure to use our Full PlasmidSeq/Long PCRSeq for sequencing.

  1. Enter our webshop
  2. Click on Tubes or Plates under "Full PlasmidSeq / Long PCRSeq" and follow the further instructions

For more detailed instructions, please consult Microsynth’s User Guide.

FAQ

How can I judge the quality of the received sequence?

We supply additional information that allow you to identify problematic regions and evaluate the overall sequencing quality:

  • In the *.variable.tsv file that opens with Excel, all residues of the contig are listed that show a rate >10% of mismatches, deletions and/or insertions. These values are based on all the reads that were used to create the contig. You may sort the list according to % mismatches, % deletions, or % insertions to identify the regions within your plasmid that might be problematic or ambiguous. The coverage, as well as base quality of the reads at the respective position are also indicated.
  • In the *.cleaned.html file of the addendum you can see a statistics of the reads that were used for producing the assembly, which comprises number of reads, length of reads and quality score of reads.
The results indicate mutations in critical regions, which potentially could delay the projects planned with the plasmid. How can I be sure that the mutations are real?

Please consult the additional information to judge the sequence quality at the position. For critical applications we recommend you to double check the sequence with an orthogonal sequencing method such as Sanger or Illumina.

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