Genome Nexus aggregates variant annotation from various sources. There are two types:
Small sized annotations are stored as static data in the mongo database directly, see the genome-nexus-importer repo if you want to update/change this data.
Larger annotation sources are pulled on the fly from other APIs and cached in the mongo database.
For a list of all supported variant annotation sources see this Google Sheet:
The code for the backend can be found here: https://github.com/genome-nexus/genome-nexus.
Clients in various languages can be generated to access it. See API
The frontend of the website is here: https://github.com/genome-nexus/genome-nexus-frontend.
The main consumer of the Genome Nexus REST API is cBioPortal. cBioPortal provides visualization, analysis, and download of large-scale cancer genomics data sets. Variants in cBioPortal are annotated using Genome Nexus. The other examples in the figure are potential other consumers. See also: Tools
There is a command line tool to annotate MAF and VCF files, see API