Welcome to Arvados^™!

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.
• 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://playground.arvados.org. If you are using a different Arvados instance replace https://playground.arvados.org 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.

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