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De novo Assembly
- Chromosome level assemblies: Generate genome assemblies for even large polyploid genomes.
- Polyploid genomes: Our expertise lies in assembling large, polyploid genomes up to 22 Gbp in size.
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Genetic variance studies, marker development, and pre-breeding: We offer additional resources to apply your de novo assembly results.
Client Project: Computomics performed a de novo assembly of two indica elite rice lines using both Illumina and PacBio data. We constructed a genetic map using 2000 F2 generation individuals to build pseudochromosome level assemblies with >95% of the scaffolds in chromosomes and >99% gene space cover.
De novo Annotation
- Explore biological function: Assess isoforms and reveal biological pathways.
- Trait mapping: Map traits to genomic positions and assess the severity of mutations in coding regions.
- Re-annotate existing assemblies: Reveal new isoforms and non-coding RNAs.
Client Project: Using machine learning-based gene finding tools on over 40 RNASeq datasets, we annotated four reference genomes of closely related species. These tools allow us to quickly annotate your genomes from closely related species - some projects completed in just a few hours.
Transcriptomics
- Differential gene expression: Utilize RNASeq data to discover trait-relevant regulation.
- Combine multiple data sets: Enhance comparative analysis by combining datasets regardless of the sequencing technology.
- Transcriptional dynamics: Explore transcriptional dynamics in plant growth and stress response.
Client Project: We compared more than 400 different RNASeq samples from seven different tissues of a polyploid crop. Using PacBio IsoSeq, we accurately determined more than 1000 novel transcript isoforms. Plant immune response genes were found to be the fastest-evolving gene family in this project.
Genotyping and Genome Graphs
- Develop new markers: Develop thousands of new markers across the entire genome.
- Low cost: We genotype polyploid species, even without a reference genome, at low cost.
- Unbiased marker discovery: Get a complete overview of every part of the genome.
- Customization: We customize the setup of your genotyping projects for each genome, species, population size for the marker amount you require.
- Correlate traits to gene expression data: Identify traits linked to large structural variants and correlate then with gene expression data.
-
Accelerate selection: Build haplotype blocks or a genome graph to compare hundreds of varieties
Client Project: We called variants in over 400 lines of a polyploid crop and developed suitable markers for allele-specific PCR. For any project, we continuously perform all genotyping using the same, customized parameters. This makes results comparable and reproducible.
Genomic Selection: Predicting Phenotypes
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Predict performance: Learn how your hybrid will perform before it is field-tested.
-
High throughput: Genotype millions of genetic markers in thousands of plant lines.
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Responsive analysis design: Receive Breeding Values within 24 hours and improve the model with each cycle.
Client Project: We performed reference-free genotyping of four stages of a breeding program to determine which locations are most predictive for the entire region. This reduced the number of regions needed for early-stage selection from eleven to just three, freeing up space and saving costs.
Metagenomics and Microbial Genomics
- Simultaneous visualization: Identify species, genes, transcripts, and metabolic networks simultaneously.
- Fast and specific: Analysis of raw data of 1.8 billion reads to visualized results in only two days.
- Explore complex communities: Investigate complex microbial communities without the need for time-consuming culturing.
- Correlate traits to gene expression data: Identify traits linked to large structural variants and correlate then with gene expression data.
Client Project: We compared dozens of microbial samples, considering gene content, metabolic pathways, and taxonomy. The speed of our award-winning alignment tool allowed annotations using multiple reference databases. We delivered results in several formats to ensure future accessibility and immediate utility.
Epigenomics
- Define breeding strategies: Cutting edge methods of epigenome profiling allow you to easily define plant breeding strategies.
- Identify new markers: Develop non-genetic markers and explore novel epialleles modulating traits
- Identify gene expression regulators: Quickly identify regulators of gene expression and detect loci of adaptive stress responses.
Client Project: Using MethylScore, we accurately identified discrete DNA methylation differences of short-term heritability in response to hyperosmotic stress that was associated with transcriptional and phenotypic changes. We determined that these acquired adaptations were sensitively found in non-CG contexts only.
De novo AssemblyDe novo Assembly
- Chromosome level assemblies: Generate genome assemblies for even large polyploid genomes.
- Polyploid genomes: Our expertise lies in assembling large, polyploid genomes up to 22 Gbp in size.
-
Genetic variance studies, marker development, and pre-breeding: We offer additional resources to apply your de novo assembly results.
Client Project: Computomics performed a de novo assembly of two indica elite rice lines using both Illumina and PacBio data. We constructed a genetic map using 2000 F2 generation individuals to build pseudochromosome level assemblies with >95% of the scaffolds in chromosomes and >99% gene space cover.
De novo AnnotationDe novo Annotation
- Explore biological function: Assess isoforms and reveal biological pathways.
- Trait mapping: Map traits to genomic positions and assess the severity of mutations in coding regions.
- Re-annotate existing assemblies: Reveal new isoforms and non-coding RNAs.
Client Project: Using machine learning-based gene finding tools on over 40 RNASeq datasets, we annotated four reference genomes of closely related species. These tools allow us to quickly annotate your genomes from closely related species - some projects completed in just a few hours.
Transcriptome StudiesTranscriptomics
- Differential gene expression: Utilize RNASeq data to discover trait-relevant regulation.
- Combine multiple data sets: Enhance comparative analysis by combining datasets regardless of the sequencing technology.
- Transcriptional dynamics: Explore transcriptional dynamics in plant growth and stress response.
Client Project: We compared more than 400 different RNASeq samples from seven different tissues of a polyploid crop. Using PacBio IsoSeq, we accurately determined more than 1000 novel transcript isoforms. Plant immune response genes were found to be the fastest-evolving gene family in this project.
GenotypingGenotyping and Genome Graphs
- Develop new markers: Develop thousands of new markers across the entire genome.
- Low cost: We genotype polyploid species, even without a reference genome, at low cost.
- Unbiased marker discovery: Get a complete overview of every part of the genome.
- Customization: We customize the setup of your genotyping projects for each genome, species, population size for the marker amount you require.
- Correlate traits to gene expression data: Identify traits linked to large structural variants and correlate then with gene expression data.
-
Accelerate selection: Build haplotype blocks or a genome graph to compare hundreds of varieties
Client Project: We called variants in over 400 lines of a polyploid crop and developed suitable markers for allele-specific PCR. For any project, we continuously perform all genotyping using the same, customized parameters. This makes results comparable and reproducible.
Genomic SelectionGenomic Selection: Predicting Phenotypes
-
Predict performance: Learn how your hybrid will perform before it is field-tested.
-
High throughput: Genotype millions of genetic markers in thousands of plant lines.
-
Responsive analysis design: Receive Breeding Values within 24 hours and improve the model with each cycle.
Client Project: We performed reference-free genotyping of four stages of a breeding program to determine which locations are most predictive for the entire region. This reduced the number of regions needed for early-stage selection from eleven to just three, freeing up space and saving costs.
MetagenomicsMetagenomics and Microbial Genomics
- Simultaneous visualization: Identify species, genes, transcripts, and metabolic networks simultaneously.
- Fast and specific: Analysis of raw data of 1.8 billion reads to visualized results in only two days.
- Explore complex communities: Investigate complex microbial communities without the need for time-consuming culturing.
- Correlate traits to gene expression data: Identify traits linked to large structural variants and correlate then with gene expression data.
Client Project: We compared dozens of microbial samples, considering gene content, metabolic pathways, and taxonomy. The speed of our award-winning alignment tool allowed annotations using multiple reference databases. We delivered results in several formats to ensure future accessibility and immediate utility.
EpigenomicsEpigenomics
- Define breeding strategies: Cutting edge methods of epigenome profiling allow you to easily define plant breeding strategies.
- Identify new markers: Develop non-genetic markers and explore novel epialleles modulating traits
- Identify gene expression regulators: Quickly identify regulators of gene expression and detect loci of adaptive stress responses.
Client Project: Using MethylScore, we accurately identified discrete DNA methylation differences of short-term heritability in response to hyperosmotic stress that was associated with transcriptional and phenotypic changes. We determined that these acquired adaptations were sensitively found in non-CG contexts only.
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Initial Consultation
Experimental Design
Quotation
Data Generation
Final Report & Presentation
Feedback
Progress Report
Analysis
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Collaborations with Academic Institutions
University of Tübingen
Tübingen, Germany
Max Planck Institute for Developmental Biology
Tübingen, Germany
Swiss Federal Institute of Technology in Zurich
Zurich, Switzerland
Collaborations with Companies
Gene Expression
Zurich, Switzerland
Nebion creates a next-generation genomic search engine for discovery research, target and marker prioritization.
NEBION AG and their product GENEVESTIGATOR
Next-generation Sequencing
Tübingen, Germany
CeGaT is a Next-Generation Sequencing service provider.
Center for Genomics and Transcriptomics —
CeGaT GmbHSequencing Instruments
Menlo Park, CA, USA
PacBio develops sequencing solutions for scientists that propel the field of genomics, improve science and research, and create positive impact globally.
Memberships
United Nations Global Compact
New York, USA
The UN Global Compact is a call to companies to align strategies and operations with universal principles on human rights, labour, environment and anti-corruption, and take actions that advance societal goals.
Baden Württemberg Connected e.V.
Stuttgart, Germany
The main goal of the network organization is to foster key-technologies in order to strengthen the region's economic development.
Crop Science Society of America
Madison, WI, USA
Crop scientists focus on improving crops and agricultural productivity while effectively managing pests and weeds.
Verein zur Förderung der Biotechnologie und Medizintechnik
Tübingen, Germany
This society helps regional companies and research instituts to strengthen the position of the region as a distinguished location for biotechnology and medical engineering.
Erfolgsfaktor Familie
Berlin, Germany
Computomics is a family-friendly employer, providing flexible work hours, part-time options and offers parental leave months.
Awards
Science2Start Ideenwettbewerb 2011/2012
Baden-Württemberg, Germany
The Science2Start Ideenwettbewerb prices scientists and founders for life-science-concepts with economic potential.
Innovation Award 2015
Baden-Württemberg, Germany
Selects regional industrial, technical and technological service companies for exemplary efforts in the development of new products, methods and technological service or the use of modern technology in products, production or service.
CyberOne 2014
Baden-Württemberg, Germany
The CyberOne Hightech Award Baden-Württemberg is looking for technology-oriented start-ups with innovative business concepts.
Innovative through Research
The network is a common initiative of companies and foundations that advises, connects and supports in the areas of education, science and innovation.
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Methods
Here, we give references to relevant methods authored by Computomics team members and collaborators.
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Contact
×Tübingen, Germany
Computomics is based in the university town of Tübingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics GmbH
Christophstr. 32
72072 Tübingen
GermanyPhone: +49 7071 568 3995
info@computomics.com×Madison, Wisconsin
Computomics is based in the university town of Tübingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics Corporation
2858 University Ave #222
Madison WI 53705
USAPhone (858) 832-4036
info@computomics.com×Davis, California
Computomics is based in the university town of Tubingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics Corporation
140 B St, Ste 5-371
Davis CA 95616
USAPhone (858) 832-4036
info@computomics.comTübingen, Germany×Tübingen, Germany
Computomics is based in the university town of Tübingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics GmbH
Christophstr. 32
72072 Tübingen
GermanyPhone: +49 7071 568 3995
info@computomics.comMadison, Wisconsin×Madison, Wisconsin
Computomics is based in the university town of Tübingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics Corporation
2858 University Ave #222
Madison WI 53705
USAPhone (858) 832-4036
info@computomics.comDavis, California×Davis, California
Computomics is based in the university town of Tubingen, situated in the Southwest of Germany, but serves clients all over the world. We also have offices in Davis, California and Madison, Wisconsin.
Computomics Corporation
140 B St, Ste 5-371
Davis CA 95616
USAPhone (858) 832-4036
info@computomics.com- © Computomics GmbH 2016
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- Your Privacy
