We Offer Data Analysis Services Centered Arround De novo Assembly and Long-read Sequencing

For all our services, we not only offer to perform the entire analysis but also do consulting and troubleshooting. If you have any questions, please do not hesitate to contact us.

De novo assembly of single genomes and metagenomes

Depending on your research question you may need complete, high-quality and gap-free assemblies generated with the latest third-generation sequencing technologies. Or you might be satisfied with a draft assembly which gives you enough information about your organism of interest.

For a wide range of organisms as well as for metagenomes, we can generate state-of-the-art assemblies using appropriate technologies.

de novo assembly of prokaryotic and viral genomes

By choosing the right sequencing and assembly strategy, viral, prokaryotic, and mitochondrial genomes can most often be readily assembled in a relatively quick time and at low cost. Depending on your needs, we can provide strategies on how to generate high quality assemblies with an extremely low error rate using the most suitable sequencing technologies.

Find here some examples of publications from Genexa team members successfully generating these types of assemblies.

de novo assembly of eukaryotic genomes

Generating high-quality genome assemblies of eukaryotes can be quite a challenging task. A large genome size and a high degree of ploidity as well as large genomic repeats are the main reasons for this. However, applying modern long-read sequencing technologies such as Pacific Biosystems® SMRT® Sequencing and Oxford Nanopore Technologies® nanopore sequencing, Genexa can help you to overcome this challenge!

Learn more about the technologies Genexa applies to solve these assembly problems here.

de novo assembly of metagenomes

Amplicon-based metagenomics can be helpful to provide you with an overview of the taxonomic diversity in your metagenomic sample. However, with amplicon-based methods you do not get detailed information about aspects such as metabolic potential or antibiotic resistance of the organisms in your sample. Also, you will only detect taxonomic groups which you target during amplification.

For this reason a whole genome assembly of your metagenome can be highly valuable.

See here an example of a study which involved Genexa team members assembling a metagenomic sample near completely using third-generation sequencing technologies.

Resequence or compare genomes – detect variation or unique genes in your organism of interest

resequencing & variant detection

There are many reasons to resequence your species of interest, no matter whether it involves the entire genome or a targeted region.

You might not be convinced about the quality of an already available assembly since it may be fragmented or contains many assembly errors. It might also be of interest to compare your mutant or strain to a reference genome to find potential causes for different phenotypes.

Depending on your research question, it may be advisable to use long-read sequencing to detect large scale miss-assemblies or rearrangements. Or you could go for short reads and do SNV detection.

Contact us if you are not sure which strategy is the right one for you.

comparative genomics

Comparing genomes can answer important questions such as:

Are specific genes or gene variants linked to a phenotype of interest?
Which genes are conserved in all examined genomes?
Which genes are unique? Are they useful as marker genes or do they have a relevant role in the metabolism of the organism?
Are there any new functional clusters such as operons compared to a closely related organism?

Please find here an example of a study which involved Genexa team members assembling and comparing genomes of lactic acid bacteria.

Make sense of your genome sequence – annotation and other downstream analyses

de novo genome annotation

Once you have your genome assembly done, the next important step is to de novo annotate your genome. Genexa has experience in annotating prokaryotic, mitochondrial and viral genomes.

The annotation can be done de novo on the entire genome or by re-annotating a specific site which has been modified or was miss-assembled in a previous assembly.

other analyses & quality assessments

There are many more analysis services we can offer – too many to list them all. If you are interested in a specific analysis, just contact us and we can have a chat!

We are also happy to do an evaluation of an existing analysis or genome assembly in case you are not sure about its quality or correctness.