---
layout: default
navsection: userguide
title: Welcome to Arvados!
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_If you are new to Arvados, please read the "Getting Started":{{site.baseurl}}/start/index.html guide for a quick introduction to working with 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":{{site.baseurl}}/user/tutorials/tutorial-keep.html content-addressable cluster file system.
* Running compute-intensive genomic analysis pipelines, such as alignment and variant calls using the "Arvados Crunch":{{site.baseurl}}/user/tutorials/intro-crunch.html cluster compute engine.
* Storing and querying metadata about genome sequence files, such as human subjects and their phenotypic traits using the "Arvados Metadata Database.":{{site.baseurl}}/user/topics/tutorial-trait-search.html
* Accessing, organizing, and sharing data, pipelines and results using the "Arvados Workbench":{{site.baseurl}}/user/getting_started/workbench.html web application.

This User Guide goes into more depth than the "Getting Started guide":{{site.baseurl}}/start/index.html, covers how to develop your own pipelines in addition to using pre-existing pipelines, covers the Arvados commandline tools in addition to the Workbench graphical interface to Arvados, and can be referenced in any order.

The examples in this guide use the Arvados instance located at <a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}</a>.  If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.

Curoverse maintains a public Arvados instance located at <a href="https://workbench.qr1hi.arvadosapi.com/" target="_blank">https://workbench.qr1hi.arvadosapi.com/</a>.  You must have an account in order to use this service.  If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com.

h2. Typographic conventions

This manual uses the following typographic conventions:

<notextile>
<ul>
<li>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 '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black.  For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
<pre><code>~$ <span class="userinput">ls foo.*</span>
foo.input foo.output
</code></pre>
</li>

<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
<li>Bold text emphasizes <b>specific items</b> to review on Arvados Workbench pages.</li>
<li>A sequence of steps separated by right arrows (<span class="rarr">&rarr;</span>) 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.
</li>
</ul>
</notextile>