Genome analysis

BaseClear offers complete solutions for both De Novo genome analysis and re-sequencing projects. With our many years of experience, highly qualified specialists and innovative technologies we can assist you with even the most challenging genome sequencing projects. We provide complete start-to-finish project management with customized analysis and data reporting possibilities. Our highly qualified staff is always willing to discuss your project to see how we can help you reach your research goals as fast and efficient as possible.

Expertise in microbial genome analysis

We have completed many projects involving human, animal and plant genomes. However, our main focus is on microbial genome analysis (bacteria, Archaea, fungi, yeast, algae and viruses). We have completed thousands of bacterial, fungal and virus sequencing projects. Bacterial genomes we have sequenced include the species E. coli, Bacillus, Lactobacillus, Lactococcus, Actinomycetes, Deinococcus, Staphylococcus and Neisseria. Fungal genomes we have sequenced include the species S. cerevisiae, Aspergillus and Tricoderma. Furthermore, with our virus sequencing and assembly services we have succesfully analysed ssDNA, dsDNA, ssRNA and dsRNA viruses, such as Influenza and Adenovirus.

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BaseClear Microbiology services

Complete microbial strain characterization

Genome sequencing is an essential tool for strain development and optimization of microorganisms used as food ingredients or as production strains. BaseClear offers significant expertise and years of experience in complete microbial strain characterization. Our options for strain characterization include:

  • Complete genome based strain characterization as required for EFSA or FDA claims
  • Unique antibiotic resistance gene screening based on a highly curated CARD database
  • Plasmid detection and identification services
  • Production strain analysis including copy number and gene expression analysis
  • Fungal production strain analysis and annotation
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Microbial strain characterization


In order to reach the highest quality genome sequence for De Novo projects, we usually recommend a combination of long (PacBio or Nanopore) and short (Illumina) sequencing technologies which are assembled using state-of-the-art computation algorithms. The long sequence reads comprise the information to generate a proper draft genome architecture, whereas the high-quality Illumina short reads can be used for polishing in order to generate a final assembly of highest quality at both a structural and sequence level. Final gaps (if needed) can be closed using for instance Sanger sequencing.

Advanced pipeline for high throughput genome analysis projects

We have developed a high throughput bacterial sequencing platform which is capable of sequencing literally hundreds of genomes per week. This platform is a combination of in-house developed library preparation solutions, robotics, genome sequencing and several automated bioinformatic pipelines. We can tailor this bacterial sequencing pipeline to your research question and think with you to minimize the cost of sequencing while maximizing the output. Additional options like an annotation of the whole strain collection and view the genomes in a browser will allow you to search for specific genes or enzymes.

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Optional bioinformatics

BaseClear offers standard and custom downstream bioinformatics services for bacterial and fungal sequencing projects. For De Novo sequencing this includes genome assembly, bacterial genome annotation and fungal genome annotation. For fungal or bacterial re-sequencing projects our customers can opt for our comparative genomics solutions, including variant detection and whole microbial genome alignments.

Genome assembly and annotationComparative genomics

Why choose our genome sequencing service?

  • Optimal sequencing strategy for De Novo sequencing projects based on a combination of long read and short read technologies
  • Optimized and automated workflows for high quality results with fast and guaranteed delivery times
  • Extensive experience with microbial genome sequencing, over the last years we have sequenced tens of thousands of microbial genomes
  • Fast and guaranteed delivery times with our premium services
  • Bioinformatics expertise for assembly, annotation, SNP detection, etc.
  • Interactive online platforms to analyse and visualize your data
  • Excellent support from our microbial genome sequencing experts
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Testimonial DSM Biotechnology centre

For our bacterial and fungal sequencing projects 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.

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