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For genomes that need to be sequenced for the first time, we developed our De Novo Genome Analysis service. With our many years of experience, highly qualified specialists and state-of-the-art technologies we can assist you with even the most challenging De Novo sequencing projects. We can provide complete start-to-finish project management with customized analysis and data reporting. Our highly qualified staff is always willing to discuss your project to see how we can help you reach your research goals as fast as possible.


In order to reach the highest sequence quality, we recommend a hybrid strategy combining long (PacBio or Nanopore) and short (Illumina) sequencing technologies with the latest computation algorithms. The long sequence reads provide a genome assembly with the best structural quality and the lowest number of contigs. Next, we use the high-quality Illumina short reads for assembly polishing in order to generate a final assembly of highest quality at both structural and sequence level. Final gaps (if needed) can be closed using for instance direct Sanger sequencing.


We have completed many projects involving human, animal and plant genomes. However, our main focus is on microbial genomes, including bacteria, fungi, yeast, algae and viruses. We have sequenced and assembled hundreds of thousands  of microbial genomes. Bacterial species we have sequenced include E. coli, Bacillus, Lactobacillus, Lactococcus, Actinomycetes, Deinococcus, Staphylococcus and Neisseria. Fungal species include S. cerevisiae, Aspergillus and Tricoderma. Furthermore, we have sequenced and assembled many viral genomes with either DNA or RNA genomes, such as Influenza and Adenovirus.

Fill in our contact form to discuss your microbial genome sequencing project with one of our specialists. 


  • Optimal sequencing strategy based on a combination of long read (Nanopore or PacBio) and short read (Illumina) sequencing technologies
  • Expertise in microbial genomes
  • Experience with project sizes ranging from single to thousands of genomes
  • Multiplex options available to sequence as efficient as possible
  • Fast and guaranteed delivery times with our premium services
  • Many satisfied customers worldwide 


BaseClear offers standard and custom downstream bioinformatics services for De Novo sequencing projects, including genome assembly and annotation. Read more about these possibilities on our assembly and annotation page.

Meet Adalberto Costessi!

Adalberto is Product Manager Next Generation Sequencing and responsible for the development of new applications and technologies.

Testimonial DSM Biotechnology Centre

BaseClear offers a good performance from a technical perspective. I really appreciate the open way in which we communicate and whenever we need something done urgently, they are always willing to discuss the possibilities and try to help us make deadlines. They offer advice on the best set-up of the project and concentrate on finding solutions, instead of only pointing out potential problems.

Associate Scientist Bioinformatics


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