Frequently Asked Questions
About GreenGate Genomics
Working with us
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 firstname.lastname@example.org.
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 email@example.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 firstname.lastname@example.org 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.
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:
- 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
- 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.
- At GreenGate Genomics you get the support of a team of bioinformatic experts, covering a range of special competences.
- 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 email@example.com or our contact form.
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.