Fabian Engelniederhammer
TNG Technology
Analytical database for sequences
RhyDB stores genomic sequences and their metadata in a relational format. Its declarative query language (similar to SQL) supports fast filtering, aggregation and queries on nucleotide and amino-acid sequence alignments.
RhyDB query languageExecute
default
.filter(region = 'Europe')
.map({"S[69]" := S.at(69), "S[70]" := S.at(70), "S[501]" := S.at(501)})
.groupBy({count := count()}, {pangoLineage, "S[69]", "S[70]", "S[501]"})
.orderBy({count.desc()})
.limit(10)Get started
Read the documentation and tutorials, work through exercises or query a live RhyDB instance.
Read
Documentation
Read about the core concepts, learn with the interactive tutorials or look up the reference.
Browse documentation →
Practice
Exercises
Write queries against a live instance and compare your answers with reference queries.
Start an exercise →
Use
Console
Connect to a public RhyDB instance or query your own data directly from the browser using WebAssembly.
Open the console →
Features
RhyDB is an open source, relational and analytical database. It specializes on sequence alignments, allowing big datasets to be queried in real time. It further offers various features relevant for genomic epidemiology such as searching lineage systems and trees.
Query sequences
Filter substitutions, deletions and insertions; find co-occurrence patterns, and more.
Filter, join and retrieve
Retrieve filtered records, download only the fields you need, and join multiple tables.
Scalability
RhyDB is used for huge datasets including 10 million SARS-CoV-2 whole genome assemblies and 800 million raw reads from wastewater
Institutions and funding
The core team is based at the cEvo group at ETH Zurich and at the Swiss Institute of Bioinformatics (SIB). We received funding from ETH Zurich, the US CDC's Office of Advanced Molecular Detection (OAMD) and NIH* through the Pathogen Data Network.
* This resource is supported as a whole or in part by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under grant n°U24AI183840, awarded to the SIB Swiss Institute of Bioinformatics. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Contact
Feedback, suggestions, bug reports and active contributions are highly welcome, please create an issue in our Github repository. For general questions, please contact Alexander Taepper (alexander.taepper@bsse.ethz.ch) and Chaoran Chen (chaoran.chen@bsse.ethz.ch). For media requests, please reach out to ETH Zurich Media Relations (mediarelations@hk.ethz.ch).