Fast and Professional NGS data analysis

You are an expert in coming up with new research questions. We are experts in finding the answers from your next-generation sequencing data. From quality control of raw NGS data to publication-grade figures, we have you covered. Probably faster than you would expect.

Why outsource NGS data analysis?

Success in life science research requires seamless collaboration with a service-oriented bioinformatics team. We developed our model to answer to this still largely unmet need — we call it Bioinformatics as a Service, and it comes with the following benefits:

  • The analysis workflow is tailored to your data and research questions
  • An allocated team of professional bioinformaticians enables fast and high-quality analysis
  • A dedicated project manager ensures fluent communication throughout the project
  • The results are carefully explained to you and discussed
  • All methodology is clearly described to allow publishing

Data types and analyses

We apply THE LATEST methods for testing hypotheses or exploring large data sets, and even develop new methods when needed. In addition to analyzing data from next-generation DNA-sequencing and RNA-sequencing experiments, we have experience from most array and mass-spec assays out there. Read more

The project workflow

The scientific content of each project is unique, but the workflow — especially for our academic customers — follows a standard pattern.

1. Pre-project meeting

First we discuss your research and propose NGS experiments and bioinformatics analyses that would suit your needs. If we believe collaboration would be fruitful, we draft a project plan and present a quote for a project including the specifications, schedule and price.

2. Next-gen sequencing (if required)

We can help you acquire NGS experiments from the most convenient and cost-effective sequencing service provider. If you already have the data, we may skip this phase and move straight to the the next one.

3. Data delivery

The customer or their sequencing service provider delivers us the data on an external hard drive to our office. If the files are small or the network connection very fast and stable, then file sharing services, or uploading the files to our server over Secure File Transfer Protocol (SFTP), is an option, too.

4. Kick-off meeting

After receiving the data and a sample sheet linking all data files to pertinent metadata, a dedicated project manager reviews the files, background information such as publications, and schedules a kick-off meeting to agree on the first steps before starting the actual analyses.

5. Quality control analysis

Unless we receive QC'd data, we perform a throrough QC analysis for all samples, summarize and report the data quality to you, and discuss any possible quality issues. If required, we wait for you to generate new data.

6. Basic analysis

After ensuring data quality, we run an analysis pipeline to, e.g., assemble the genome or transcriptome, estimate gene expression levels, find genetic variants or epigenetic events. The genes, loci or variants are annotated, statistically compared between sample groups and visualized. We present these intermediary results to you in a teleconference and agree on the downstream analyses. Again, if your data has already been processed to this level, we may begin with the downstream analyses.

7. Downstream analysis

More tailored analyses are run to answer your research questions. This step typically involves pathway and regulation analyses, integrating different data types, comparing your data to publicly available data sets, and associating molecular events to biologically or clinically relevant variables using regression and machine learning techniques.

8. Reporting results

After performig the contracted analyses, we sit down with you to carefully explain what we did and what do the results mean. After presenting the results, we might still reformat or modify the figures and tables according to your wishes. Then, we provide you with a project report including result tables, figures, and methods descriptions.

9. Publishing findings

We can provide additional consulting in the manuscript preparation and submission phase as well. Re-running analyses, reformatting figures to comply with the guidelines of a specific journal and writing methods descriptions are the typical needs in this step. Eventually, if manuscript reviewers have bioinformatics-related questions, we can address them by elaborating and justifying the computational methodology.

References

OUR NEW CUSTOMERS come to us primarily through referrals from current ones. This means that customer satisfaction is our first priority. Based on our experience, making a customer happy — not to mention exceeding their expectations — requires not only scientifically sound NGS data analysis and a rapid turnaround, but clear, honest and frequent communication. Read more

Frequently asked questions about our NGS data analysis service:

  • Do I have to define the analysis in detail to receive a quote?
    • You do not have to be able to define the contracted bioinformatics work in detail. We just have to understand how the data was generated, and what are your research questions. Then, we plan the computational analysis accordingly and provide you with a quotation based on the plan. That said, if you do have detailed specifications for the analysis, we can write an offer based on them just as well.

  • Do you have experience working with researchers in my specific field?
    • It is likely. Our bioinformaticians come from a range of backgrounds from plant science to cancer genomics, and our customers throughout the years span almost every corner of the academic and industrial life sciences. While every research project is unique as a whole, we have probably dealt with data sets, analyses and research questions similar to yours. Upon discussing a project with you, we do want to let you know more about our experience with similar projects and customers.

  • Can I change the project contents after you have begun the analysis?
    • To quite a great degree, yes. During the project we keep you up to date on the progress, and might wish to discuss data quality or intermediary results with you, so that we can agree on the final deliverables. We are happy to adapt to what we see in the data and to your changing requirements as long as they are in line with the resources that were allocated to the project in the original quote. You will have a dedicated project manager to be in contact throughout the project for any such inquiries.

  • How do I deliver the data to you?
    • The most convenient way for delivering large data, such as raw NGS files, is sending them on an external hard drive to our office (Mr Klaus Breitholtz, Genevia Technologies Oy, Hämeenkatu 14 C 33, 33100 Tampere, Finland). Just make sure you have local copies of the files as a backup before sending the data. If the files are small or you have a very fast and stable network connection, then file sharing services, or uploading the files to our server over Secure File Transfer Protocol (SFTP), is an option, too.

More questions and answers

Hear what our customer says about our NGS data analysis service

Let's talk!

Leave your email address here with a brief description of your needs, and we will contact you to get things moving forward!

Antti Ylipää
Antti Ylipää CEO, co-founder Genevia Technologies Oy +358 40 747 7672
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