> ## Documentation Index
> Fetch the complete documentation index at: https://docs.cosmosid.com/llms.txt
> Use this file to discover all available pages before exploring further.

# API Documentation

> The bioinformatic pipelines within the Cosmos-Hub can be accessed via the Command Line through API integration.

Using the command line, you can seamlessly integrate CHAMP™, Kepler, and more into your automated workflows and operations while also leveraging our cloud infrastructure.

This guide will provide step-by-step instructions for running each of our workflows via the command line. You can find additional information on our CLI at [https://github.com/CosmosID/cosmosid-cli/blob/master/README.md](https://github.com/CosmosID/cosmosid-cli/blob/master/README.md).

<CardGroup cols={2}>
  <Card title="Install and Setup" icon="download" iconType="solid" horizontal href="https://docs.cosmosid.com/docs/api-reference/install-and-setup" />

  <Card title="Running the CLI" icon="terminal" iconType="solid" horizontal href="https://docs.cosmosid.com/docs/api-reference/running-the-cli" />

  <Card title="Example Commands: Running CHAMP" icon="code" iconType="solid" horizontal href="https://docs.cosmosid.com/docs/api-reference/example-running-champ" />

  <Card title="Example Commands: Running 16S ASV" icon="code" horizontal href="https://docs.cosmosid.com/docs/api-reference/upload_16s" />
</CardGroup>