Frequently Asked Questions

To develop a global, ‘Always-On’ pathogen monitoring ecosystem that will revolutionise infectious disease prevention and treatment. We will be able to predict and prevent future pandemics, advance precision medicine and develop point-of-care diagnostics to improve outcomes and save lives.

Quality & Speed

It automates and speeds up analysis, providing a thorough, accurate, and reliable understanding of pathogens within minutes instead of hours.

Cloud Data Management

We offer automated, reliable, and accurate processing. Capable of extensive automation, including APIs, our platform offers a range of flexible implementation options. Built on Oracle Cloud Infrastructure, privacy and security are at the heart of the design, ranging from data encryption to the latest developments in human read removal to minimise personally identifiable information. Our scalable cloud platform enables rapid analysis, accelerates results, and produces detailed reports.

Simplicity and Ease of Use

As an individual, you can create a Personal Account:

1. Click on Get Started

2. Navigate to EIT Pathogena and click on “Sign Up”. Follow the instructions to create a user account.

3. After completing the sign-up form, you will receive an email with instructions to set up your account password.

4. Once your password is set, you'll receive a verification email. Click the link in the email to verify your account and email address. If you don’t receive the email, please contact pathogena.support@eit.org.

You are now ready to start.

For organisational sign-up, contact pathogena.info@eit.org.

• E.coli

• Staphylococcus aureus

• Klebsiella spp.

• Anicetobacter baumanii

• Shigella spp.

• Streptococcus pneumoniae

• Neisseria gonorrhoeae

• Salmonella spp

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The platform supports both Illumina and Oxford Nanopore Technology (ONT) FASTQ files. If you have other platforms in mind that you would like to use, please get in touch with us. We are committed to expanding our support and are open to accommodating your specific needs to enhance your research and collaboration experience. Your input helps us continually improve and provide the best possible service. 

For Mycobacteria, our platform can process data for about 100 samples in an hour. For SARS-CoV-2, it can process 100 samples in 20 minutes. 

For individuals: Any intellectual property rights in the data and content you upload to, create, or generate using the Pathogena Web Portal and Services, including the results, belong to you. You and your licensors retain ownership of all intellectual property rights in your materials and uploaded data.

We grant you a worldwide, non-exclusive, non-assignable, and non-transferable royalty-free license to copy the deliverables during the term of this agreement. This license is for personal, non-clinical academic, and research purposes only. You cannot sub-license, assign, or transfer these rights to any third party. For more details, see our End User License Agreement (EULA).

For organisations: data ownership is defined in a separate agreement.

EIT Pathogena Bioinformatic Analysis Platform is designed with privacy and security at its core. Built on the secure infrastructure of Oracle Cloud, it adopts a robust approach to securing all customer data. It also empowers users to ensure all personal data is anonymised prior to upload by using our command line tool. Alternatively, users can opt to upload genomic data directly to the portal, with data anonymisation and human read removal processes being completed shortly after upload.

Our approaches to security follow industry best practice including ensuring data is encrypted as rest and in transit, our engineers have segregated roles and we follow the principle of least privilege where access is only granted as necessary to deliver the service. EIT Pathogena utilises several autonomous products to ensure security patches are applied to services in a timely manner.

The data is hosted in the data centre of Oracle Cloud in London, UK. Please contact us for other data residency requirements.

When you submit samples for processing this will include FastQ files and summary information about the sample such as dates and approximate geographic location.

Personally identifiable information could be uploaded into the system if a FastQ file contains human reads or if a subject name is included in the file name for example. If data does not contain human reads, then the web portal upload can directly process samples without concern. However, we also have a command line tool which can be used to remove human reads and submit the sample data for processing.

We currently does not re-analyse samples once uploaded. However, you may re-upload the same sample to be analysed with the newest released updates.

Individuals can access the data they uploaded.

For organisations: members of organisation based on their user role and data sharing within or external to the organisation as specified. In order to provide the services, and in line with the End User Licence Agreement, Ellison Oxford Limited employees and approved third-party contractors who provide support may access data on limited occasions to provide, support and improve the services.

There are multiple ways to upload data into the platform. This enables you to have full control over PII. If your sample data contains genomic PII, you can use our command line tool for human read removal prior to upload.

Alternatively, you can drop and drag files directly into the portal. Once uploaded, they will immediately have human reads removed, and the original files will be deleted.

Data is processed within an Oracle data centre in London, UK. Please ensure that you are aware of any local legal requirements on the handling of your data prior to uploading.

Signing up as an organisation with EIT Pathogena provides several valuable benefits. Firstly, it allows your designated team to access a centralised platform where all your sample analyses are stored. This centralisation simplifies data management and ensures that all team members can easily find and use the necessary results.

When you sign up, you can assign different user roles within your organisation. There are two user roles available: Standard and Super users. Standard users can access only the sample data they uploaded themselves or those explicitly shared with them. On the other hand, super users have broader access, enabling them to view all samples within the organisation.

If requested by the organisation, Super users are able to share data within their own organisation or with external organisations. This flexibility fosters collaboration and efficient data sharing within teams and external partners. Both Standard and Super users can see data shared from external organisations.

The procedure to sign up is straightforward. Simply contact us and provide the details of who you want to add to your team. We will guide you through the setup process, ensuring that your organisation is ready to take full advantage of the platform's features.

We actively seek to work with organisations and researchers to drive innovation and achieve shared goals. By partnering with us, you can leverage our expertise and resources, access advanced data-sharing tools, and participate in groundbreaking projects. If you are interested in exploring collaboration possibilities, please contact us to discuss how we can work together to advance our mutual interests.

The SARS-CoV-2 analysis pipeline, designed for sequences obtained via tiled amplicon sequencing, includes consensus genome assembly, pangolin lineage assignment, and identification of related isolates. It is fast—processing a batch of 100 samples in just 20 minutes—robustly tested (with a preprint in progress), and supports multiple amplicon schemes.

Individual users will be required to read and sign an End User Licence Agreement (EULA).

Organisations will require a Master Services Agreement (MSA).

EIT Pathogena supports and encourages the publication of academic papers based on results from EIT Pathogena Bioinformatics Analysis Platform.

In the event that you make public any results or any data obtained from the results, please include a statement identifying and acknowledging the use of the EIT Pathogena Web Portal and any contributing organisations in the development of such results.

For the avoidance of doubt, only results and not raw shared data can be published.

Please include the following wording in any such publication: “With thanks to the support of EIT Pathogena in this work, and [if relevant] to [the organisations] who chose to share their data.”