Whole Metagenome Shotgun Sequencing

Insights into all phenotypic features

Next to microbial quantification using 16S sequencing, GenomeScan provides full microbial genome analysis. This provides you insight into all genotypic features or other variable characteristics.

Profiling of whole microbial genomes leads to a more detailed taxonomic classification of all bacteria and other microorganisms in your sample. You can make the distinction up to species and subspecies level when the total DNA is analyzed instead of solely the V4 region of the 16S ribosomal gene.

At GenomeScan we can offer the choice between short (Illumina) and long-read (PacBio) sequencing. Illumina sequencing instruments reads short ~150 bp fragments, which allows for fast and high throughput analysis. The PacBio Sequel sequences long stretches of DNA, up to 60 kb. Human or other eukaryotic DNA can be selectively removed before bacterial full genome profiling. Our scientists have designed a hybridization capture method to remove methylated DNA residues, which efficiently depletes the host DNA.

We help you with choosing the right methods

Depending on your research question and purity of your sample, our scientists can provide you with the optimal method to visualize the microbiome and their traits. For example, antibiotics resistance cassettes can be directly linked to the (sub)species. Resistant bacteria can be detected with a high accuracy and sensitivity, which is especially important for clinical applications.

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Best taxonomic classification option due to the alignment of the whole genome
GS check icon Product page   Whole Metagenome Sequencing
Linking of phenotypic features with species
GS check icon Product page   Whole Metagenome Sequencing
Classification down to species and subspecies level
GS check icon Product page   Whole Metagenome Sequencing
Publication-ready figures


GenomeScan BioIT experts have set up data-analysis pipelines for efficient processing of whole metagenome sequencing data, either for short-read or long-read sequencing. Sequential steps include data trimming and preparation for alignment to the NCBI reference database to determine the characteristics and relative abundancies of different microbial populations. Depending on your research question, the bio-informatics specialist will generate a report with ready-to-present data.

The basis of the report consists of a comprehensive table containing the various microbes that were detected. It displays the taxonomic rank, genome size and number of reads that classifies the various microorganisms. Krona-plots provide an interactive tool to visualize the composition of the sample.

We have summarized key information about our whole metagenome sequencing service into a product specification sheet, which you can download here.

Discuss your project with us

We have years of experience in the field. Talk with us about best practices and how we can help your research.


Competitive pricing for
unmatched quality

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