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ABOUT

GreenGate Genomics is a spinout project that is currently being incubated at the GFZ German Research Centre for Geosciences in Potsdam (GER) as part of the Helmholtz Enterprise Initiative. GreenGate Genomics is  led by a group of five researchers and entrepreneurs with extensive experience in the fields of environmental and molecular microbiology, microbial genomics, computational biology, and bioinformatics.

OBJECTIVE

GreenGate Genomics is offering services in genomic and bioinformatic analyses with special expertise in microbiology and molecular biology. GreenGate’s services support scientists, institutes and companies through customized data analysis, the creation of analysis workflows and pipelines, and/or the development and implementation of bioinformatic training and workshops.

Application of the correct and most suitable bioinformatic wofkflow is essential to avoid data analysis and data interpretation challenges and opimize downstream processing. Accurate analysis of NGS sequencing often requires individualized and case specific binformatic tools and pipleines. Some of the typical bioinformatics workflows commonly used in academia and industry environmental and molecular microbiology research are outlined below:

SERVICES

To get a quote for your project contact us with the type of services you are interested in and we will get in touch with you shortly!

DNA based services

AMPLICON DATA BASED SERVICES

  • Barcode primer check
  • Library preparation
  • Arrange sequencing
  • Demultiplexing samples
  • Quality control, decontamination and chimera filtering
  • Taxonomic assignment
  • Community data (in OTU or ASV format)
  • Krona plot 
  • Functional prediction based on 16S rRNA gene data

METAGENOMIC SERVICES FOR ILLUMINA SHORT READ DATA

We can perform Nanopore Minion sequencing in our lab and can conduct work as follows:

  • Library preparation prior to sequencing
  • Sequencing
  • Effective raw reads calling with powerful GPU
  • Quality control on sequencing data
  • Assembly and gene calling
  • Genomic binning to MAGs
  • Taxonomic and functional annotation
  • Pathway analysis
  • Phylogenetic tree of MAGs

METAGENOMIC SERVICES FOR OXFORD NANOPORE LONG READ DATA

  • Raw data (paired-end or single-end) quality check
  • Decontamination
  • Assembly short reads to contigs (long reads)
  • Gene calling, quantification from contigs
  • Genomic binning (Metagenome-Assembled Genomes, MAGs) and taxonomic assignment
  • Functional annotation for genes on contigs or MAGs
  • Pathway analysis based on contigs or MAGs
  • Phylogenetic tree of MAGs
RNA based services

METATRANSCRIPTOMIC ANALYSIS SERVICES (Illumina)

  • Raw data (paired-end or single-end) quality check
  • Assembly and gene calling
  • Functional and taxonomic annotation of genes
Other services

CONSULTATION SERVICES

  • Consultation on experiment design
  • Data analysis strategy
  • Recommendation of right sequencing platform suitable to answer your question
  • Quotation of service

DOWNSTREAM ANALYSIS AND BIOSTATISTICS

  • Rarefaction and rank abundance curve
  • Alpha diversity and beta diversity
  • Indicator species
  • Generalist and specialist species
  • Dissimilarity measure calculations (e.g. Bray-Curtis, Euclidian, Jaccard distance)
  • Ordination (e.g. PCA, CA, NMDs, PCoA, CCA)
  • Correlation with environmental and chemical measurements
  • Network analysis (dissimilarity- or correlation-based) 
  • Module/cluster identification from network
  • Data visualization in various format (e.g. bubble plot, heatmap, Venn diagram, Chord diagram, Sankey or custom advance plots)
  • PERMANOVA (e.g. adonis, db-RDA)
  • Mantel test
  • LEfSe (Liner discriminant analysis effect size) differential abundance analysis
  • Structural equation modelling (Path analysis, confirmative factor analysis)

ACESSORY SERVICES

  • Raw data download from your service company
  • Data submission to Archive database (e.g. SRA, ENA, DDBJ)
  • Raw data storage on local machine
  • Reference database for specific genes, proteins or taxonomic groups
  • Manuscript assistant in bioinformatics and statistics
  • Cooperation (e.g. bioinformatic partner) in funding application

Team

Alexander Bartholomaeus PhD, Chief Executive officer (CEO):

Alex leads the GreenGate Genomics team, overseeing projects and guiding strategic management and business development. He is also involved in day-to-day operations and contributes to bioinformatic analyses and consulting.

Alex has 10 years of experience in bioinformatics, programming, genomics, and software development. He also has a strong background leading and supervising bioinformatics projects. Former roles include academia, research and development and industry positions.

Sizhong Yang, PhD, Chief Technical Officer (CTO):

Sizhong is responsible for the day-to-day operations at GreenGate Genomics, working on bioinformatic analyses and software development. He also has extensive experiences in wet-lab experiments with good understanding of experiment prioritization, such as sample treatments, sequencing steps, appropriate statistical analyses to implement to ensure robust and reproducible results.

He has 10 years of experiences in environmental/industrial microbiology and bioinformatic workflow development. He has performed a diverse range of project-oriented bioinformatic analyses, data visualization and interpretation, as well as extensive knowledge and experience of biostatistics.

Daniel Lipus, PhD, Chief Customer Officer (CCO):

Daniel manages outreach and marketing at GreenGate Genomics, he is responsible for public relations and represents the first contact for potential customers.

In addition, he is involved in strategic decision making and business development.   He has 8 years of international experience in environmental/industrial microbiology and with bioinformatic workflows and has worked and consulted on genomic and bioinformatic projects. He has strong ties to the US, having occupied both academia and government positions.

Susanne Liebner, Prof. Dr., Scientific Advisor:

Susanne is working group leader at the German Research Centre for Geosciences (GFZ) and, since 2020, professor for Terrestrial Environmental Microbiology at the University of Potsdam. She has about 15 years of experience in molecular environmental microbiology, specifically on the complexity of soil and sediment microbiomes. Her team uses various bioinformatic pipelines, a wide array of multivariate statistics and data‐mining approaches. For GreenGate Genomics, Susanne provides access to her network and professional background. 

 

Dirk Wagner, Prof. Dr., Scientific Advisor and Founder:

Dirk is head of the Section Geomicrobiology at the German Research Centre for Geosciences and Professor for Geomicrobiology and Geobiology at the University of Potsdam. He is an expert in geomicrobiology with more than 20 years of experience in studying microbial life in terrestrial environments using classical microbiological approaches and modern molecular biological tools. As scientific advisor, he supports GreenGate Genomics by his long-years of experience in coordinating and managing international projects as well as his experience in working with medium-sized companies.

Case Studies

  • Atacama Desert

GreenGate wishes to showcase its extensive and specialized bioinformatic portfolio and is actively seeking partners and clients to  pilot its services. Working with us as part of a pilot project offers the unique opportunity to receive a high quality bioinformatic service. If you are interested in such a partnership we are happy to meet and discuss how to provide our bioinformatic expertise to your project in more detail.

Here we show one-page case studies to give you a nice overview of our expertise and possible projects.

Nanopore Genome Sequencing

  • Evaluation of Oxford Nanopore Technologies (ONT) base calling options
  • Careful execution of different computational steps from basecalling to binning of final genome.
  • Some steps of this workflow have a high influence on the size and quality of the final genome.
  • Read more …

Plastisphere

  • Isolation and Oxford Nanopore Sequencing of six different bacterial strain isolates from plastic polluted landfill soil
  • Reconstruction of metagenome assembled genomes (MAGs)
  • Taxonomic classification of recovered genomes
  • Functional annotation allowed the discovery of specific genes involved in polyethylene degradation (PE) degradation
  • Read more … 

Atacama Desert

  • Evaluation of extracellular and intracellular DNA fractions in soil and rock samples from different Atacama desert locations
  • 16S rRNA amplicon sequencing and reconstruction of microbial community patterns
  • Identification of highly adapted microbial species to investigate their response to extreme aridity and UV exposure, and gather important insights on microbial turnover in Mars like environments.
  • Read more … 

Biocide Resistance

  • Differential gene expression analysis  of Pseudomonas biofilms in response to sodium hypochlorite
  • RNA-seq and Transcriptome data analysis
  • Identification of significantly up- and down regulated genes
  • Reconstruction of potential resistance pathways
  • Read more …

Deep Biosphere

  • Reconstruction of Microbial distribution patterns across a 230m terrestrial subsurface drill core
  • Application of specifically adapted laboratory and bioinformatic workflows for low biomass environments
  • Amplicon and metagenomic based taxonomy analysis
  • MAG recovery and annotation allowed detection and characterization of CO2 utilizing methanogenic and chemolithotrophic microorganisms
  • Statistical evaluation provided insights into microbial co-occurrence patterns and bio-geo interactions.
  • Read more …

Methane-Cycling Microbiome in Permafrost

  • Taxonomic and functional profiling of methane cycling microbiomes in permafrost soil
  • Characterization of microbial diversity via 16S rRNA amplicon data analysis
  • Evaluation of active microbial populations by targeting microorganisms contributing to greenhouse gas (CH4 and CO2) production
  • Read more …

Oil and Gas Ecology

  • Investigation of microbial abundance and composition s patterns in oil and gas wells to identify the potential for bio-corrosion and well fouling
  • 16S rRNA and metagenomic sequencing to reconstruct microbial distribution and diversity
  • Assembly and annotation of metagenomic data to identify metabolic potential
  • Reconstruction and characterization of draft genomes provided insights into cellular processes in oil and gas environments.
  • Read more …

FAQs

Frequently Asked Questions

About GreenGate Genomics

Services

Expertise

Working with us

ABOUT GREENGATE GENOMICS

Is GreenGate Genomics an independent operating company?

At the moment GreenGate Genomics is a startup project, which is located at the GFZ German Research Center for Geosciences in Potsdam, Germany. We are being supported by the Helmholtz Enterprise Initiative. The people working for GreenGate are highly qualified bioinformatic and microbiological scientists with special expertise in the areas of environmental and molecular microbiology.

Who is the official contract partner at this stage?

Currently we are in our pilot-project phase and a contract or research agreement for a service by GreenGate Genomics will be set up between you and the GFZ German Research Center for Geosciences. The GFZ is a one of the world’s most renowned research centers for Earth Sciences and part of the Helmholtz Association of National Research Centers. Working with the GFZ in this phase allows GreenGate Genomics to offer bioinformatic services at research collaboration costs.  If you want to know more details about this contract structure contact us at info@greengategenomics.com.

SERVICES

What kind of services do you provide?

We offer our customers a wide range of bioinformatic services, designed to support their analysis of genomic (next generation sequencing) data. This includes standard analysis, such as taxonomic analysis of amplicon data or metagenomic assembly and binning, but also fully customized analysis workflows, which we carefully select based on the dataset and the customers’ requirements. You can find a full list of our services on our service overview page.

For customers who wish to run their own analysis, we offer a variety of software packages, which we can distribute and that can be installed locally with our support. For all request, please use our contact form or email us at info@greengategenomics.com

 

I cannot find the type of analysis I am interested in on the service page, do you offer it?

On the service page we list the most commonly employed type of bioinformatic analysis requests and workflows. If you cannot find the type of analysis you are interested in, please contact us directly at info@greengategenomics.com with your request and we will get back to you quickly.

 

Do you offer bioinformatic training or workshops?

If you commission a bioinformatic pipeline/workflow with us this usually includes a training session to help you install, implement and run these tools. We will be by your side to troubleshoot and make sure the delivered pipeline provides the desired results and outputs. Depending on the service package we agreed upon we will update your pipeline on a regular basis.

In addition, we provide individual training sessions for specific workflows (e.g. 16S amplicon data analysis or metagenomic binning) to help you become familiar with frequently employed bioinformatic analysis. Please contact us with your request to find out more about this service and get a quote.

Finally, GreenGate Genomics offers workshops on relevant bioinformatic topics on a regular basis. Please follow us on twitter @greengategenom or visit our website for announcements and our workshop schedule.

 

Do you support grant application writing and manuscript preparation?

Yes, we can provide an initial consultation on what bioinformatic analyses would be suitable for your project and what would be the best way to implement them. We can provide you with cost and time estimates and even do some preliminary data analysis to strengthen your hypotheses.

We can also prepare method sections describing bioinformatic analyses that were conducted in case of a paper manuscript or that will be conducted as part of a future project.  In addition, we can consult you on the best ways to present and interpret your genomic data in a manuscript for peer reviewed journal publication.

EXPERTISE

Why should we/I work with GreenGate Genomics?

With the advent of next generation sequencing platforms, genomic analyses have become one of the most important tools in modern microbiology, resulting in vast amounts of genomic sequencing data being generated on a daily basis. However, as the sequencing of genetic material has become easier and cheaper, accurate analysis of the generated sequencing data remains one of the biggest bottlenecks in this research field. Special bioinformatic expertise and experience are required to process genomic data correctly and obtain high quality results applicable for scientific publications, reports and diagnostics. With an unlimited and confusing number of programs, software and scripts available across various repositories and websites, selecting the right analysis strategy is a challenging task for non-expert users.

With the experts at GreenGate Genomics at your side you can be sure to get the most out of your genomic data. With our know-how we can precisely support your project, develop the most suitable analysis strategy and select the most useful bioinformatic tool set. We are always keeping up to date in the rapidly changing landscape of bioinformatic tools, so that our customers can be sure to have their data analyzed with the most accurate, scientifically proven and accepted workflows and software solutions.

 

Why not hire a bioinformatician?

Hiring someone with expertise in the field of bioinformatics seems to be the first thought when having to analyze genomic data without any in house expertise. However, there are several reasons why outsourcing this analysis step and working with GreenGate Genomics might be the better choice:

  1. Hiring a well-qualified, full time bioinformatician can be expensive. Next to the costs for salary and recruitment, an appropriate workspace (office, computational hardware and software) needs to be considered
  2. Working with GreenGate Genomics, you only pay for the analyses you actually need and when you need them. If your team/project does not generate enough genomic data to occupy a full time bioinformatician position, looking for external help is the most time and cost-efficient approach.
  3. At GreenGate Genomics you get the support of a team of bioinformatic experts, covering a range of special competences.
  4. Having a bioinformatician work for you means additional administrative and management work. A bioinformatician might also leave the position at any time, while working with an external provider guarantees you a reliable partner that delivers when needed.

 

Do you have the right expertise for my project?

At GreenGate Genomics we focus on the bioinformatic data analysis in the field of environmental and molecular microbiology. We have extensive experience working in these areas, and believe to distinguish ourselves from other providers specifically with our know-how working with genomic datasets from challenging environmental samples. Nevertheless, we have the expertise and capability to process genomic data from a wide variety of sources and samples. Every project is unique and if you wish to find out more about what type of analysis we have conducted visit our case studies page or contact us directly via info@greengategenomics.com or our contact form.

WORKING WITH US

How do I find out how much an analysis or a software solution cost?

The cost of an analysis conducted by us or a pipeline developed by us depends on the amount of data, type of analysis and other requirements, which can best be determined by a quick meeting. If you are interested in working with us send us a brief email with your request (e.g. what analysis, number samples, etc.). Depending on the extent of your inquiry we will quickly send you a cost estimate. Otherwise we will ask you for a short meeting (free of charge) to get more details on your project. Based on this exchange we will then put together an offer for your requested service.

How do I make sure my data is not being misused and that I will main intellectual property of the project?

GreenGate Genomics respects your privacy, holds no rights to the data and does not share the data with any third parties. If you wish, we will set up a Non-Disclosure Agreement (NDA), regulating the transfer and use of your data.

What do I get at the end of a project?

The final output of a project depends on the deliverables that were agreed upon at the start. In the case of bioinformatic analysis we provide you with different types of tables and figures as well as descriptions of the employed workflows. This information will be provided to you in a report or on request as individual files.

If we developed a workflow/pipeline for you we will provide you with the necessary files to install the software on your computer. There are different ways the software can be distributed to you (Docker, Conda) and this will be agreed upon at the start. In addition, we will provide the relevant documentation for the software and offer a training session to support the installation, familiarize you with the application, and be available for any troubleshooting.

If data processed by GreenGate Genomics get published, do you need to be listed as an author?

We do the analysis for you, but do not require a co-authorship. If possible, it should be mentioned that the data was processed by an external provider, GreenGate Genomics, in the methods section. If you wish us to help you prepare the manuscript and contribute to the interpretation of the data we are happy to help and can then be listed as a co-author. You can find a list of papers we authored/co-authored here. Please discuss these details with us in our consultation meeting, so we can accommodate your request.