In the last years we have specialized in microbial genome analyses, of both Whole Genome Sequencing (WGS) and metagenomic samples.

We have developed dedicated pipelines for a broad spectrum of bacterial analyses, aimed at basic research as well as clinical, agricultural and biotechnological applications.

Our facility is well equipped for simultaneus analysis of hundreds and thousands of bacterial samples, using the leading software in the field.

Our services include:


Whole Genome Sequencing (WGS)

Analysis of DNA sequence reads obtained from isolated bacteria:

  • Quality assurance and de novo assembly of raw sequence reads
  • Gene prediction and functional annotation of the assemblies
  • in silico molecular typing at species and sub-species levels, including MLST and Core Genome MLST (cgMLST) analyses
  • SNP calling and construction of SNP-based phylogenetic trees
  • Generation of Minimum Spanning Trees from SNP, MLST, cgMLST and concatenated core gene sequences
  • Identification of virulence and antimicrobial resistance determinants
  • Molecular epidemiology and outbreak investigation
  • Comparative genomics and biomarker development


Metagenomics - amplicon sequencing (16S and 18S rRNA, ITS etc.)

Analysis of sequence reads obtained from PCR amplification of marker genes from bacterial communities / environmental samples:

  • Quality assurance and preprocessing of the raw sequence reads
  • Identification of the taxa present in environmental samples and their relative abundance (OTU picking and generation of a BIOM table)
  • Assessing the degree of species diversity in each sample (alpha diversity analysis)
  • Comparative analyses among samples (beta diversity analyses)
  • Statistical testing for differential abundance of individual taxa among the samples
  • Advanced downstream analyses such as functional analyses, association networks, source tracking and more


Metagenomics - shotgun sequencing

Analysis of DNA (or RNA) sequence reads obtained from bacterial communities / environmental samples:

  • Quality assurance and preprocessing of the raw sequence reads
  • Taxonomy, abundance and diversity analyses as described for amplicon sequencing
  • Gene prediction and functional classification
  • De novo assembly of individual genomes from the metagenomic samples, followed by gene prediction, functional annotation and molecular typing
  • Identification of virulence and antimicrobial resistance determinants