Welcome to Arvados™!

If you are new to Arvados, please try the Quickstart on the documentation homepage instead of this detailed User Guide.

This guide provides a reference for using Arvados to solve big data bioinformatics problems, including:

  • Robust storage of very large files, such as whole genome sequences, using the Arvados Keep content-addressable cluster file system.
  • Running compute-intensive genomic analysis pipelines, such as alignment and variant calls using the Arvados Crunch cluster compute engine.
  • Storing and querying metadata about genome sequence files, such as human subjects and their phenotypic traits using the Arvados Metadata Database.
  • Accessing, organizing, and sharing data, pipelines and results using the Arvados Workbench web application.

The examples in this guide use the public Arvados instance located at https://cloud.curoverse.com. If you are using a different Arvados instance replace https://cloud.curoverse.com with your private instance in all of the examples in this guide.

Typographic conventions

This manual uses the following typographic conventions:

  • Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted command to enter (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type ls foo.* while in your home directory and the expected output will be "foo.input" and "foo.output".
    ~$ ls foo.*
    foo.input foo.output
    
  • Code blocks inline with text emphasize specific programs, files, or options that are being discussed.
  • Bold text emphasizes specific items to review on Arvados Workbench pages.
  • A sequence of steps separated by right arrows () indicate a path the user should follow through the Arvados Workbench. The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.

Next: Arvados Community and Getting Help

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.