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Full PlasmidSeq – Whole Plasmid Sequencing with ONT

Full PlasmidSeq: State-of-the-Art Plasmid Sequencing Service
 
 
Submit purified DNA up to 300 kb or an E. coli liquid culture containing a plasmid up to 25 kb. No primers or prior sequence information are required. You receive the complete, annotated plasmid sequence. Optionally, provide a reference sequence to identify sequence variations – at no additional cost.

NEW: Skip plasmid preparation and submit your E. coli liquid culture directly. We isolate the plasmid before sequencing.
 

Choose Your Starting Material

Requirement Purified DNA E. coli liquid culture
Accepted material Plasmids, BACs, phages and linearized plasmids Turbid culture (OD600 >0.5) containing a homogeneous plasmid population
Maximum size Up to 300 kb Plasmids up to 25 kb
Required amount ≥15 µl at 20 ng/µl Tubes: 300 µl; plates: 150 µl per well
Preparation Purified DNA supplied by customer Plasmid preparation performed by Microsynth
Important information Non-prepaid service required above 50 kb
(size range 50 - 125 kb and 125 - 300 kb)		 Non-pathogenic BSL-1 strains only; surcharge applies
Turnaround time 1–2 working days after sample arrival at your regional Microsynth laboratory (<50 kb) Results by noon on the second working day after arrival at Microsynth Seqlab in Göttingen*

*E. coli samples are processed at Microsynth Seqlab in Göttingen. Samples submitted through another Microsynth location are forwarded internally. Please allow approximately 1–2 additional working days for transport, depending on the submission location.

What You Can Achieve

  • Sequence circular or linearized plasmids and BACs in a single experiment
  • Obtain the full plasmid sequence in a single experiment
  • Verify plasmid integrity and detect unwanted mutations
  • Compare your plasmid against a reference sequence and identify sequence variations
  • 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 de novo assembled plasmid sequence (.fasta)
    • Sequence with corresponding quality scores (.fastq)
  • 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
    • 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 Reference-Based Analysis – Free of Charge
    • Upload or select a reference sequence during ordering
    • Alignment of sequencing reads to the provided reference sequence
    • Reference-based analysis provided in addition to the de novo assembly, at no additional cost
    • Identification of sequence variations, including substitutions, insertions, and deletions
  • Optional
    • Complete raw reads (*rawreads.fastq.gz) available on request

Turnaround Time

  • Purified DNA: Results within 1–2 working days after sample arrival at your regional Microsynth laboratory
  • E. coli liquid cultures: Results by noon on the second working day after arrival at Microsynth Seqlab in Göttingen
  • Results are delivered Monday to Friday

Use our Microsynth drop boxes for free and convenient shipment.

E. coli samples submitted through Microsynth Switzerland, Austria or France are forwarded internally to Göttingen. Please allow approximately 1–2 additional working days for transport, depending on the submission location.

How to Order

Need Full PlasmidSeq Labels?

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

Already Have Labels?

  1. Enter our webshop
  2. Click on Tubes or Plates under Full PlasmidSeq / Long PCRSeq
  3. Register your samples, optionally upload or select a reference sequence, and complete your sequencing order.

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

FAQ

How can I judge the quality of the received sequence?

The .overview.html report provides an overview of your sequencing results, including read depth, coverage, and mapping statistics.

For a more detailed evaluation, the .uncertain.xls file lists positions where the combined mismatch, insertion, and deletion rate exceeds 10%. These positions may indicate sequencing uncertainties and should be examined more closely.

Additional read quality statistics, including read lengths and quality scores, are available in the .rawreads.html file.

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.

When will I receive my Full PlasmidSeq results for E. coli samples?

Results are generally available by noon on the second working day after the sample arrives at our sequencing laboratory at Microsynth Seqlab. Samples submitted through a regional Microsynth location require additional transit time to the sequencing laboratory.

Please allow approximately one additional working day for samples submitted in Switzerland or France. Transit times for other locations may vary.

Can I compare my plasmid sequence to a reference sequence?

Yes. During ordering, you can upload a reference sequence or select a previously uploaded sequence. In addition to the de novo assembly, you will receive a reference-based analysis that identifies differences between your plasmid and the provided reference, including substitutions, insertions, and deletions. This analysis is provided at no additional cost.

Testimonials