Comparative genomics

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

At BaseClear, we are committed to offer results that meet the highest standards in the field. Therefore, based on scientific reviews by independent research groups, our experts developed a state-of-the-art variant detection pipeline. Our standard variant calling service is based on the BBMap aligner (Bushnell B.) and FreeBayes variant caller (Garrison et al. 2012), and includes low-frequency variant detection. Variant detection using NGS generally includes the following steps:

  • Alignment of NGS reads to one or more references
  • Detection of single or multiple nucleotide variants (SNPs or MNVs)
  • Detection of short insertions and deletions (InDels)
  • Annotation of variants based on the reference (e.g. gene location, amino acid change, etc.)

Our pipeline is tested on an extensive number of microbial genomic datasets including both in silico simulated data and real-life sequencing data from well-characterized microbial strains with references available. Amongst the species included were Escherichia coli, Streptococcus mutans, Staphylococcus aureus, Lactobacillus casei, Bordetella pertussis, Bacillus cereus, and Kluyveromyces lactis.

Deliverables of the BaseClear variant detection service

  • Alignment files and indices (in BAM BAI formats)
  • List of variants (in VCF format)
  • Consensus sequence (in FASTA format)
  • Variants effect table (in  CSV, i.e. Excel, format)
  • Reports and statistics (in PDF format)
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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).

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