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A major challenge in biotechnology is to find genetic explanations for differential phenotypic behaviour between strains. Why is strain A more effective in converting a glucose substrate than strain B? Why is strain 1 more resistant to antibiotic treatment compared to other 9 strains? Which genes or gene clusters are shared between a group of strains (i.e. the pan or core-genome)?

At BaseClear use a combination of powerful analysis to address these questions. At this moment we offer standard whole genome alignments and variant detection services. 


BaseClear has years of experience with variant detection. With this service you will receive the reference alignments in BAM format, the sorted alignment index files in BAI format, the consensus sequences in FastA format and a table containing detailed information on found variants: SNPs (single base substitutions), SUBs (multiple-base substitutions) and insertions and deletions. A summary of the found variants and alignment statistics is presented in a variant detection report. 

Example of a read alignment


  • Quality filtering and trimming of reads in order to start the analysis with high-quality sequences
  • Reference alignment is performed using the state-of-the-art aligner of the CLCbio Genomics Workbench.
  • Variant calling is also performed with the quality-based algorithm of the CLCbio Genomics Workbench.
  • Stringent parameters are used among which:
    - Quality score evaluation of the alignment position and surrounding bases.
    - Usage of forward-and-reverse mappings.
    - Limited allowance of mismatches.
    - Coverage and multi (redundant) hit removal
  • The final output is provided in comprehensive Excel tables, which can be customized for multiple samples (to easily compare different samples)

Example of a SNP table 


Our Whole genome alignment (WGA) provides more insight into the different genomic architecture between genomes. In brief, sequence alignments are constructed between a number of genomes and the output consists of a comprehensive overview of structural variations that lie at the basis of differential functional behaviour. This analysis can be performed by customers themselves using our online BaseClear Genome Explorer: the Compare module features a unique tool to compare multiple genomes through alignment and interactively analyse genetic variations between sequenced genomes. This enables our customers to easily perform in-depth analysis on-the-fly, without the need of buying expensive analysis tools!

It is important to remark that this analysis differs from the Variant detection service which is performed using short-read mapping (and focuses on small differences) whereas in the WGA option assembled genomes are aligned with each other (and focuses on larger variations).

The BaseClear Genome Explorer is an online portal that allows interactive genome comparisons. Unique regions or genes are easily detected and displayed within the graphical interface. Access is free for BaseClear customers. 


The Whole genome comparison (WGC) module is our latest release and allows customers to compare hundreds of genomes  based on the composition of orthologous groups. It does not compare genomes at a nucleotide level. In brief COG orthologous groups are predicted using the OrthoMCL method (Li et. al, 2003) and subsequently compared between the genomes. The input therefore consists of a number of annotated genomes, whereas the output is an (online available) interactive Pivot table showing the absence or presence of orthologous groups in each sample. As a result the customer can easily find out how biological processes (e.g. Energy production and conversion, carbohydrate metabolism and transport) are genetically encoded in each sample. It is important to mention that phenotypical data (or meta-data) can be added on-the-fly! Finally the BaseClear Genome Explorer allows the construction and display of a phylogenetic tree thus showing the taxonomic relationships between all samples.

This great new service is provided in collaboration with our partner NIZO food research 

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.


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