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BaseClear offers complete bioinformatics packages for genome analysis (e.g. for De Novo or re-sequencing projects) and our managers are happy to discuss the ideal workflow that best fits your needs and budget. Analysis are generally offered in combination with our Next Gen sample preparation and sequencing services, but also if you already have sequencing data available we can be of assistance with our bioinformatics solutions. Standard bioinformatics solutions include assembly, annotation and comparative analysis... but tailored-made strategies are also offered. Our main drive is to make sure that your main research questions are answered.

A schematic overview of a genome analysis workflow: Illumina and PacBio reads are assembled into a finished genome followed by in-depth annotation. The annotated genomes are imported into our secure online portal which allows the customer to interactively mine and compare genomes. 


Our bioinformatics department has developed state-of-the-art assembly pipelines which follow a reference-based or De Novo approach (and in some cases a combination of both). The ultimate goal is to provide our customers with a high-quality finished genome sequence. To accomplish this task we offer different sequencing approaches among which Illumina HiSeq, Illumina MiSeq and PacBio RS II (with SMRT technology) platforms. The resulting reads are optimally merged into finished genomes using the best available tools in the market for draft assembly, error correction, scaffolding and gap closure. We also offer different options for quality assessment and control. 

Two examples of assembly quality control figures: in the left panel the coverage distribution of all contigs is displayed, in the right panel a BLAST-search is shown where the compact clusters indicate that the library contains a single organism (E. coli). 

Delivered output:

  • Assembled contig and scaffold sequences in FastA format.
  • Alignment file (BAM) and sorted alignment index file (BAI) in case of reference-guided assembly.
  • AGP (Accession Golden Path) file describing the linkage between contigs in the scaffolds. 
  • This format is required for WGS submissions to the NCBI.
  • De Novo assembly report containing a summary of the assembly results and quality measures.


Often a stretch of nucleotide sequence is not the ideal output format of a sequencing experiment. In such scenario BaseClear can offer high-quality annotations. In brief we first define the most likely gene structure model (for bacteria with Prodigal software and for eukaryotes with Augustus software). Subsequently we assign functional annotations to genes (inclusive of EC-, GO- and CAZy numbers) , tRNAs and rRNAs. The standard output includes GenBank and GFF files which follow the NCBI standards, but other formats can be easily provided upon request. The output can be easily viewed in any genome browser, but we are proud to offer our customers free access to our unique online BaseClear Genome Explorer. This is the perfect tool to mine and compare your genomes in an interactive manner.

Read more about the BaseClear Genome Explorer and ask for a free trial account at the “Interactive online portals” section. 

The BaseClear Genome Explorer is an online portal that allows interactive genome viewing and mining features. Gene structures are displayed in a comprehensive (graphical) manner. Access to the Genome Explorer is free for BaseClear customers. 

Delivered output:
  • Table containing full annotation for predicted coding sequence regions.
  • GenBank and GFF annotation formats.
  • Extended annotation report containing a summary of the assembly results and quality measures.
  • Free access to our online BaseClear Genome Explorer which allows interactive analyses of the results (free license valid for one year, read more at the “Interactive online portals” section) 

Meet Walter Pirovano!

Walter is director of the bioinformatics department and supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.

Testimonial DuPont Industrial Biosciences

The support that BaseClear has provided in the field of bioinformatics and downstream processing of next generation sequencing data has been extremely important for us. There are of course other organisations that offer next generation sequencing but that does not mean that you have everything you need. BaseClear's extra service is unique and represents one of their great strengths.

Senior Scientist


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