The code in this repository underlies a data infrastructure for SARS-CoV-2 genomic surveillance. It is used to generate and publish SARS-CoV-2 genome sequences from the Swiss SARS-CoV-2 Sequencing Consortium (S3C). For more information on the S3C, see our consortium web site.
The basic project workflow is to collect SARS-CoV-2 test metadata and whole-genome sequences, store the data in a PostreSQL database, annotate the data with quality control and other information, and generate submission files for upload to public sequence databases.
This repository has two high-level directories, database and automation.
databasecontains the code used to import data into and export data from our "Vineyard" database.automationcontains the code used to automate some data management and basic analysis tasks. We call these "microservices".
The microservices defined in automation are built on top of the database code.
They are deployed as Docker services on a dedicated server hosted at ETH Zurich.
The code will not run out-of-the-box for external users as certain infracstructure components, such as network shares, have to be configured accordingly.
- A database.
- Our PostgreSQL "Vineyard" database is set up as described in
database/init.sql. - The respective tables and columns are documented in
database/column_documentation.tsv.
- Our PostgreSQL "Vineyard" database is set up as described in
- Raw data.
- Whole-genome consensus sequences and associated sample metadata. These are project-specific and not included in this repository.
- External data, for example case counts and geographic mappings. Sources we use are mostly linked to from the respective import scripts.
- A containerization software. We build our automation code into Docker containers including all external dependencies, one per microservice.
- Secure server for hosting the database, running containers, and storing database back-ups.