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Bioinformatics Services

Gain highly valuable results from the latest machine learning technologies.

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At the leading-edge of biological science, data analysis can be complicated. Knowing what questions to ask, how to wield the available analytical tools and how to visualize and interpret results are all critical to your success. Computomics offers industry-leading bioinformatics services, powered by machine learning and statistical methods for large scale, complex biological data sets. Our experts combine over 100 years of experience in bioinformatics, machine learning and plant microbiology.

Computomics’ bioinformatics services has helped companies to understand complex genomic sequencing data since the inception of next-generation sequencing. We extract actionable, insightful results from your genomic, transcriptomic, proteomics, metabolomic and clinical data.

Our experts offer customer-specific pipeline developments for your specific questions, and have developed a multitude of automated analysis pipelines for fast turnaround times. Computomics accompanies you all the way, from experimental design and interpretation of the results to integration into your own system.


If you cannot find the bioinformatics service you need, contact us to discuss your project!


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Explore Complex Genomes

Our comprehensive genome analysis services help you to get the highest value from your sequencing data, from reference genome to pangenomes. Everything we have learned from past projects goes into each new project, which means your data is viewed and interpreted through highly experienced eyes. We help you to draw out the most compelling and actionable insights possible.

Computomics Benefits:

  • Highest accuracy and reproducibility
  • Most experienced knowledge of latest technologies and novel methods
  • Clearest publication-ready results and detailed reports
  • Best personalized bioinformatics service from experts who will work with you to get the most out of your data

Computomics Expertise:

  • Experience with organisms from 5kb to 20Gbp, from single stranded to octoploid
  • Experts in constructing complex polyploid genome assemblies
  • Quality control measures throughout the entire process
  • Continuously improved workflows for highest quality results
High Quality Genome Assemblies

Get high quality de novo and reference-based genome assemblies. We advise you on the most cost-efficient way to perform data generation to get an assembly of your specification, from a draft up to haplotype-resolved assemblies in pseudo-chromosome state. With the integration and combination of different data types, such as short and long read technologies, optical and genetic maps, 10x and Hi-C, we can disentangle heterozygous, repetitive and polyploid genomes.

A thorough quality check of the raw data and along the way at every step of the assembly process ensures high quality, comprehensible results.

Circos plot of two plant genome assemblies
Circos plot of two plant genome assemblies. The closely related genomes show high collinearity.
Accurate Structural Annotation
Predicted gene structure of Glutamine synthetase genes
Predicted gene structure of Glutamine synthetase genes. Accurate prediction of the gene structure is important for many downstream analyses.

We use the latest advances in gene prediction and annotation technologies, combining different sources of evidence such as RNAseq from Illumina, PacBio or Oxford Nanopore, curated protein databases and ESTs. Our machine learning-based algorithms and several quality control steps along the way deliver the most accurate gene models and will speed up your product pipeline with better and more reliable annotations. In your gene finding project we collaboratively ascertain the project objectives and discuss your organisms’ characteristics to ensure that a high quality structural annotation is developed.

Faster Functional Annotation
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AnnoScore is our proprietary, fully automated, scalable and adaptable functional annotation solution. It includes mappings to a plethora of different databases, such as metabolic pathways, gene ontologies and protein domains. With AnnoScore, we have a ready to go solution that performs functional annotation in little time and can be independently run.

Explore Pangenomes

Gain novel insights from pangenomes - the collection of sequences from individuals typically from the same species. Pangenome analyses fuel gene and marker discovery, can guide gene editing, and help charting the full genetic diversity of a species, including copy number and large-scale genetic variation.

Find out more about our Pangenome Solutions:

  • Graph Genotyping
  • Interactive Pangenome Browser

More about Pangenomes


  • Capture the genetic diversity of a species
  • Reveal hidden variations
  • Access more variations
  • Reduce reference bias in genomic analysis
  • Increase accuracy of variant calling and genotyping 

Gain Novel Insights from Large, Multi-Source Data Sets

Linking findings from multiple data sources can provide new insights into underlying biological mechanisms. Finding connections among multiple data sets from large scale studies requires highly skilled bioinformaticians, cutting-edge technologies and high-end computing infrastructure. Handling large amounts of data, providing reasonable analysis times and identifying the optimal tools from the vast pool available can be challenging. Our bioinformatics experts will work with you to identify the best workflow to answer your scientific questions and provide you with detailed reports throughout the project.

Our team of bioinformatics experts has guided large projects with hundreds of samples, time course experiments with repeated measurements per sample, and wide-ranging analyses including genomic, proteomic, metabolomic, metagenomic, phenotypic, clinical and other meta data. Examples of our expertise include the correlation of clinical outcome with genomic and proteomics data and the optimization of cell line production by linking transcriptomic and metabolomic data with cell culture conditions. Computomics can help you connect the dots between multiple data sets, identifying underlying mechanisms and correlations. We can also include new datasets into previous projects to update existing analyses.

Computomics Benefits:

  • Gain more meaningful results by connecting your data
  • Identify novel mechanisms
  • Gain access to cutting edge technologies and compute infrastructure
  • Get a service tailored to your specific scientific questions

Computomics Expertise:

  • Analysis of very large biological data sets
  • Deep knowledge of machine learning tools uniquely suited to connect multi-omics data sets
  • Statistical expertise and experience with highly complex statistical designs
  • Validated methods for highest accuracy
  • Personalized and dedicated customer services
Powerful Transcriptome Analysis

Analyze the effect of abiotic stress, biotic stress, environmental conditions, developmental stages, treatments, etc. on gene expression and/or splicing in your organisms of choice. We provide powerful, state of the art statistical analysis and easily interpretable graphical summaries. Inclusion of additional information such as pathway abundances and multi-omics data is possible as well. We support you at any stage of your project starting with the setup of an experimental design to getting involved when you already have the data at hand.

volcano plot
Volcano plot of log2 fold changes for a differential gene expression study. Significantly up- or down regulated genes are highlighted in red.
Reliable Epigenome Profiling
differentially methylated regions within a gene
Differentially methylated regions within a gene of two samples with respect to a reference. Sample B shows a higher number of differentially methylated regions in different contexts (CG, CHG, CHH) than sample A.

Identify new markers and gene expression regulators. We use bisulfite whole-genome, PacBio 5-mC, enrichment sequencing and ChIP-Seq to identify differentially methylated regions and histone modifications. MethylScore, our proprietary pipeline, performs reliable calls of differentially methylated regions and is optimized for plants. Compare results across genotypes down to individual loci with our Epigenetics Visualization and correlate differential methylation with gene expression.

Your Bioinformatics Pipeline

Do you want to perform your own bioinformatics analysis, are fed up with handling multiple individual scripts, and want a reproducible pipeline with settings that you can save and share? We have a lot of experience in developing and validating customer specific pipelines for all kinds of data handling and analysis. This includes integration in our scalable app technology MORPHEUS which is a safe and easy to use platform that automates data handling and storage as well as user management.
We can integrate your pipelines into your system or host them on a secure server on our site in Germany.


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