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 one strain more resistant to antibiotic treatment compared to 9 other strains? Which genes or gene clusters are shared between a group of strains (i.e. the pan or core-genome)? At BaseClear we use a combination of powerful analysis tools to address these questions. At this moment we offer standard whole genome alignments and variant detection services.

Variant detection

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.

Advantages of our variant detection service

  • 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)
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Whole genome comparisons

Our Whole Genome Comparison (WGC) 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 WGC option assembled genomes are aligned with each other (and focuses on larger variations).

Meet Walter Pirovano!

Walter Pirovano (PhD) is the Director of the Bioinformatics department and a member of the BaseClear Management Team. He supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.

Contact Walter

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