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Full PlasmidSeq

Microsynth’s state-of-the-art full plasmid sequencing service is based on long-read sequencing technology. It will reconstitute the sequence of your plasmid using a sophisticated bioinformatic pipeline developed by Microsynth that recreates the closed-circle plasmid sequence including annotation from the raw sequencing reads. The service is available for samples in tubes and 96-well plates.

Features and Benefits

  • Results delivered within 1 to 2 days of sample receipt
  • Results are delivered Monday to Friday
  • Use our drop box in your vicinity for free shipping of samples.
  • You can choose between prepaid and non-prepaid service.
  • Hypothesis-free sequencing of the complete plasmid.
  • No primers needed.

  • Economical way of sequencing your complete plasmid.
Complete Information
  • You will receive the annotated circular contig of your plasmid.
  • Detailed supporting information to evaluate sequence quality and identify problematic regions.
  • High accuracy.



How can I ship the samples?

Use our drop box system, or send your samples by mail.

What amount of DNA and concentrations do you need?

>15 µl at 20 ng/µl

Technical Questions

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.

I have received a plasmid including map that I have sequenced with your Full PlasmidSeq pipeline. The results communicated by you are different from my previous map. Can I call your support to discuss the discrepancies?

Please understand that we cannot provide scientific support at this level. Our support is limited to technical questions regarding sequencing quality, sample quality or technical abnormalities in the sequencing.

How can I open/view the data in certain files (eg. tsv, gbk)?

If you are working on Windows you may want to switch on viewing of file name extensions (In File Explorer under View, in the Show/hide group, select the File name extensions check box). For instance tab separated value files (.tsv) may be opened in any text editor or by drag and drop in an open but empty Excel table. Fasta (.fasta) and genbank (.gbk) files may be opened in a text editor or by specialized software.

How to Order

Procedure to order labels for our Full PlasmidSeq:
  • Enter our webshop
  • Click on Tubes or Plates under "Full PlasmidSeq / Long PCRSeq" and follow the further instructions
  • You can choose between prepaid and non-prepaid labels
Procedure to use our Full PlasmidSeq for sequencing.

  • Enter our webshop
  • Click on Tubes or Plates under "Full PlasmidSeq / Long PCRSeq" and follow the further instructions
See also Microsynth's user guide on the right side for more detailed information.


“Full Plasmid Seq successfully provided complete reads for both small (<4kb) and large (>20kb) plasmids in all five cases we tested. This service has proven particularly valuable when shared or purchased plasmids, such as those from Addgene, did not function as expected. It helped us identify errors in the plasmids or plasmid maps and hence allowed us to resolve cloning issues. Ecoli NightSeq has significantly saved us time and expenses by eliminating the need for plasmid preparation. Reads were long (>1kb) and of high quality for all five clones we tested. Moving forward, Full Plasmid Seq and Ecoli NightSeq will be our preferred methods for assembled products.”
René Schneider, Potsdam University


“Painless and fast, from submission to results in three days. Thorough archive of results. Will definitely use it again in the future!”

Joaquín Navajas Acedo, PhD, Biozentrum, University of Basel

“The sequencing performance was not only good, but great. I used to sequence plasmids myself with ONT’s MinION and know the problems. We had a plasmid analyzed at Microsynth for a test and it worked, even though we couldn’t read it with the MinION before. For several very complex plasmids we also got error-free results, although we could not quantify the DNA of these samples.”

Prof. Dr. Benjamin Lamp, Ph.D., Justus-Liebig-Universität

“Full PlasmidSeq is extremely advantageous for our company to fully sequence our plasmids. The first advantage is the final cost. Our common plasmids are more than 10kb long, so we can divide the cost of fully sequencing our plasmid by more than two! Second advantage is the time saved in sequencing tube preparation. We do not need to send 10 primers to sequence our plasmid, we just put our DNA in a tube without primers and the job is done! Another advantage is the amount of DNA required. In fact, you can sequence your entire plasmid with only 300ng! No more wasting DNA in sequencing! Last but not least, it is as easy as with the Economy Run. We just put the samples in the collection box, fill out the online form and 1 to 3 days later we have the sequencing result available online!”

Yasmine Genolet, Antion Biosciences

“Full PlasmidSeq really is a game changer for our lab. On the one hand it allows you to verify that there are no (unwanted) mutations anywhere in your plasmid, that might interfere with your experiments. On the other hand, due to its hypothesis-free approach (no primers needed), it is also a very useful tool for shared plasmids with little information on their complete sequence. On top of that, the Microsynth customer service was very quick & helpful in answering any questions we had concerning this service.”

Leonhard Schink, Biotechnology Institute Thurgau at the University of Konstanz

“Full PlasmidSeq proved very useful for the maintenance of our highly used AAV-plasmids. Without time consuming primer design and sanger assembly we received high quality reads and annotated maps for all our plasmids. Sample preparation takes just as long as you need to dilute your plasmid and walk to the next Microsynth drop box. In future we will use it for every new plasmid we construct or order.”

David Schmidt, M.Sc., Ruhr-University Bochum