Loculus

Loculus is a software package to power microbial genomial databases. Major features include:

• Upload and storage of consensus sequences and metadata using a simple web interface or a web API
• Flexible data preprocessing: Loculus comes with a Nextclade-based preprocessing that is able to align and translate sequences but it is also easy to implement and plug-in your own pipeline.
• Powerful searches: Loculus provides a user-friendly interface to search and view sequences as well as an API to query the data using LAPIS in the backend.
• Highly configurable: The list of metadata fields is fully configurable and Loculus supports both single- and multi-segmented genomes.

Loculus targets any group managing sequencing data. It can be used by small public health or research laboratories with a few members for storing their own, internal data as well as by international databases facilitating global pathogen sequence sharing.

📚 Visit our documentation website

Current state and roadmap

The Loculus software is already in a stable stage and used for production systems (see "Known instances" below) and you are welcome to explore this repository and try it out. However, please note that we are planning to revise the configuration files and the APIs before we release the official 1.0. Further, the documentation is so far quite sparse. We plan to release 1.0 with stable APIs and comprehensive documentation by the end of 2024.

If you are looking for a software to manage sequencing data and would like to know whether Loculus might be a suitable tool for you, please feel free to reach out. We would love to hear about your project and take your needs and requirements into consideration when we plan the further development.

Known instances

Pathoplexus is a new initiative to facilitate open sharing of genetic sequencing data for the ebola virus, the West Nile virus and the CCHF virus. See: https://pathoplexus.org

GenSpectrum uses Loculus internally to store sequencing data and power its interactive dashboards for analyzing and tracking variants and mutations of viruses. It is currently under development and will be released soon.

If you also host a Loculus instance and would like it to be added to this list, please reach out!

Development

Additional documentation for development is available in each folder's README. This file contains a high-level overview of the project and shared development information that is best kept in one place.

If you would like to develop with a full local loculus instance for development you need to:

1. Deploy a local Kubernetes instance: Kubernetes
2. Deploy the backend: backend
3. Deploy the frontend/website: website

Note that if you are developing the backend or frontend/website in isolation a full local loculus instance is not required. See the individual READMEs for more information.

Architecture

architecture_docs/ contains the architecture documentation of Loculus.

TLDR:

• Backend code is in backend, see backend/README.md
• Frontend code is in website, see website/README.md
• Sequence and metadata processing pipeline is in preprocessing folder, see preprocessing/specification.md
• Deployment code is in kubernetes, see kubernetes/README.md. Check this for local development setup instructions.
• Authentication is performed by our own Keycloak instance. See config in keycloak-image and realm-config. The keycloak login theme is built with a custom keycloakify build.

The following diagram shows a rough overview of the involved software components:

GitHub Actions

While the documentation is still a work in progress, a look at the .github/workflows folder might be helpful:

• backend.yml runs the backend tests and builds the backend docker image
• website.yml runs the website tests and builds the website docker image
• e2e-k3d.yml runs the end-to-end tests

Authentication

User management

We use Keycloak for authentication. The Keycloak instance is deployed in the loculus namespace and exposed to the outside either under localhost:8083 or authentication-[your-argo-cd-path]. The Keycloak instance is configured with a realm called loculus and a client called backend-client. The realm is configured to use the exposed URL of Keycloak as a frontend URL. For testing we added multiple users to the realm. The users are:

• admin with password admin (login under your-exposed-keycloak-url/admin/master/console/)
• testuser:testuser (read as username: testuser, password testuser) and superuser:superuser (login under your-exposed-keycloak-url/realms/loculus/account/)
• and more testusers, for each browser in the e2e test following the pattern: testuser_[processId]_[browser]:testuser_[processId]_[browser]
• These testusers will be added to the testGroup in the setup for e2e tests. If you change the number of browsers in the e2e test, you need to adapt website/tests/playwrightSetup.ts accordingly.
• To validate that a user exists we also created a technical user for the backend with username backend and password backend. The technical user is authorized to view users and submitting groups and in principle to manage its own account.

Group management

• Groups are entities managed by the backend, uniquely identified by a name.
• Every sequence entry is owned by the group that it was initially submitted for. Modifications (edits while awaiting approval, revisions, revocations) can only be made by members of that submitting group.
• Each user can be a member of multiple submitting groups.
• Users can create new submitting groups, becoming the initial member automatically.
• Group members have the authority to add or remove other members.
• Group members have the authority to edit all group metadata (except for group id)
• If the last user leaves a submitting group, the group becomes 'dangling'—it exists but is no longer accessible, and a new group with the same name cannot be created.
• Admin users can manually delete a submitting group directly on the DB but must transfer ownership of sequence entries to another submitting group before doing so to fulfill the foreign key constraint.

For testing we added all users declared above to the group testGroup.

Contributing to Loculus

Contributions are very welcome! Please see CONTRIBUTING.md for more information or ping us in case you need help.