# API ⚙️

A full listing of all API endpoints can be found here:

<https://www.genomenexus.org/swagger-ui.html>.

## API Clients

For access through Python/R see the notebooks here:

<https://github.com/genome-nexus/genome-nexus/tree/master/notebooks>

## Command Line Clients

There are two Command Line Clients available. One written in NodeJS which provides a simple user-friendly interface:

<https://github.com/genome-nexus/genome-nexus-cli>

There is also a Java Command Line Client which has been developed with a focus on internal processes at Memorial Sloan Kettering Cancer Center but might work for your use case as well:

<https://github.com/genome-nexus/genome-nexus-annotation-pipeline>

They are similar in terms of feature completeness

## Other Languages

The API follows the Swagger/Open API specification, so clients can be generated in most languages: <https://openapi-generator.tech/docs/generators>

## Applications build on top of the API

See the [tools section](/tools.md)


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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.genomenexus.org/api.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.