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Bioinformatics Services

Making use of the latest machine learning technologies to gain highly valuable results.

Full Service. Full Insight.

Computomics’ expertise is the application of machine learning and statistical methods to large scale, complex biological data sets. Our experts combine over 100 years of experience in bioinformatics, machine learning and plant & microbiology. We are extracting actionable and insightful results from our customers genomic, transcriptomic, proteomics, metabolomic and clinical data.

We have developed a multitude of automated analysis pipelines for fast turnaround times. In addition we have a long track record of providing customer specific pipeline developments for your specific questions. We accompany you all the way, from experiment design and interpretation of the results to integration into your own system. If you can not find the bioinformatic service you need, contact us to discuss your project!


Complex Genome Analysis Services - From Reference Genome to Pangenomes

With our comprehensive services we can help you to get the highest
value from your sequencing data.

The benefits of working with Computomics:

  • The highest accuracy and reproducibility
  • Access to latest technologies and novel methods
  • Detailed reports and publishing ready results
  • A personalized service by our bioinformatics experts who will work with you to get the most out of your data

Our expertise:

  • Experience with organisms from 5kb to 20Gbp, from single stranded to octoploid
  • We are experts in constructing complex polyploid genome assemblies
  • Various quality control measures along the whole process
  • Regularly updated workflows for highest quality results
High Quality Genome Assemblies

Get high quality de novo and reference-based genome assemblies. We advice you on the most cost-efficient way of 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: 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. The closely related genomes show high collinearity.
Accurate Structural Annotation
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, and combine 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 you organisms’ characteristics to ensure that a high quality structural annotation is developed.

Faster Functional Annotation

AnnoScore is our proprietary, fully automated, scalable and adaptable functional annotation solution. It includes mappings to a plethora of differente databases, e.g. 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.

Know Your Pangenomes

Quickly inspect QTL's, pinpoint or evaluate phenotype-associated variations or identify sub-populations in your pangenomes. Our service ranges from the generation of complex pangenome graphs to giving you unprecedented access to your pangenomes in our interactive and scalable visualization tool Pantograph. Intuitively inspect large-scale variation between complete genomes in whole chromosome views, or dive deep to single nucleotide level variation. Pantograph shows meta data of the genomes like phenotype information alongside the genetic variation thus allowing you to sort genomes by meta data or by genetic variants. Moreover, Pantograph lets you visualize and compare gene annotations from multiple genomes altogether.
Contact us to learn more about Pantograph's features and applications!

Exemplary multiple sequence alignment of 3 genomes translated into the Pantograph representation of the resulting genome graph. Pantograph visualizes diverse types of variants, from SNPs to large SVs by providing different zoom levels.

Multi-Omics Services - Gaining 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 as well as cutting edge technologies and high end compute infrastructure. Handling large amounts of data, providing reasonable analysis times and identifying the optimal tools from the vast pool available is often a challenge. Our experts will work with you to identify the best workflow to answer your scientific questions and provide you with detailed reports along the project.

 

We’ve performed projects involving hundreds of samples, time course experiments and repeated measure sampling, involving genomic, proteomic, metabolomic, metagenomic, phenotypic, clinical and other meta data. We can help you connect the dots between multiple data sets and identify underlying mechanisms and correlations. We can also include new datasets into previous projects to update existing analyses. Examples of our expertise include the correlation of clinical outcome with genomic and proteomics data or the optimization of cell line production by linking transcriptomic and metabolomic data with cell culture conditions.

Your 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 needs

Our expertise:

  • Handling and analyzing very large biological data sets
  • Machine learning tools uniquely suited to connect multi-comics data sets
  • Statistical expertise and experience with highly complex statistical designs
  • Validated methods for highest accuracy
  • A personalized and dedicated customer services
Powerful Transcriptome Analysis

Analyse 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 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 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, 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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