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Plasmid Sequencing

Use plasmid de novo sequencing to:
  • Efficiently characterize a plasmid
  • Rapidly validate your cloning experiment


Considerations before starting a plasmid sequencing project:

  • DNA quality and purity?
  • Is there host DNA contamination?
  • Sole plasmid or genome and plasmid?

Let us guide you – from design to analysis

Example projects using plasmid sequencing:

  • Mutation studies
  • Vector verifications
  • Characterization of production strains

Applications related to plasmid sequencing:

  • De novo sequencing
  • Resequencing


A typical workflow for a plasmid sequencing project is shown in the graphic below. Please note that our highly-modular processes allow you various entry and opting out options. If you outsource your entire NGS project to Microsynth or only parts of it is up to you.
For further reading please download our Flyer Plasmid Sequencing by NGS (see related downloads).


The assembly of plasmid and other small constructs such as phages allows insights into their genomic structure and the organization of their genetic content.

The first step in our assembly module is the removal of DNA sequences related to the host organism since host contaminations strongly interfere with the assembly process. After host removal the reads are assembled using the assembly software that is suited best for the job. Both, de novo approaches and reference guided assemblies are possible.

The module results in the assembled contigs along with statistics that answer the following questions:

  1. What is the overall cumulative length of the plasmid? (see Figure 1)
  2. What is the GC content of the plasmid? (see Figure 2)
  3. What is the size distribution for the assembled contigs? (see Figure 3)

Figure 1: Cumulative length of assembly.

Figure 2: GC content distribution for non-overlapping 100 bp windows of the assembled contigs.

Figure 3: Nx statistics for contig sizes.