</p>
  				<b><a HREF="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hubs Wiki</a></b>
                                </p>
				<p>
				<b><a HREF="trackDb/trackDbHub.html">Track Database Definition Document</a></b> &mdash; A reference guide for trackDb parameter definitions.
                                </p> 
          	                <p>
  				<b><a HREF="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines">Public Hub Guidelines Wiki</a></b>
                                </p>
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<!-- ========== What Are Track Hubs? ============================== -->
<A NAME="Intro"></A><BR>

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			    <TR><TD><FONT SIZE="4"><A NAME="TOC"></A><B>&nbsp; What Are Track Hubs?</B></FONT>
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				<P>
Track hubs are web-accessible directories of genomic data that can
be viewed on the UCSC Genome Browser (please note that hosting hub
files on HTTP tends to work even better than FTP).  
Track hubs can be displayed on genomes that UCSC directly supports, or on
your own sequence.
Hubs are a useful tool for visualizing a large number of genome-wide 
data sets.
For example, a project that has produced several wiggle plots of data
can use the hub utility to organize the tracks into composite and
super-tracks, making it possible to show the data for a large collection of 
tissues and experimental conditions in a visually elegant way, similar to how 
the ENCODE native data tracks are displayed in the browser.
<P>
The track hub utility allows efficient access to data sets
from around the world through the familiar Genome Browser interface. 
Browser users can display tracks from any public track hub that has been
registered with UCSC. Additionally, users can import data from unlisted hubs
or can set up, display, and share their own track hubs.
Genome assemblies that UCSC does not support can be loaded and viewed with associated data.
<P>
The data underlying the tracks and optional sequence in a hub reside on the remote 
server of the data provider rather than at UCSC. 
Genomic annotations are stored in compressed binary indexed files in bigBed, bigWig, BAM or VCF
format that contain the data at several resolutions.
In the case of assemblies that UCSC does not support
genomic sequence is stored in the efficient twoBit format.
When a hub track is displayed in the Genome Browser, only the
relevant data needed to support the view of the current genomic region are 
transmitted rather than the entire file. The transmitted data are cached
on the UCSC server to expedite future access. This on-demand transfer mechanism 
eliminates the need to transmit large data sets across the Internet,
thereby minimizing upload time into the browser. 
<P>
The track hub utility offers a convenient way to view and share very large sets
of data. Individuals wishing to display only a few small data sets may find it 
easier to use the Genome Browser 
<A HREF="hgTracksHelp.html#CustomTracks">custom track</A> utility. 
As with hub tracks, custom tracks can be uploaded to the UCSC Genome 
Browser and viewed alongside the native annotation tracks. Custom tracks can be
constructed from a wide range of data types; hub tracks are limited
to compressed binary indexed formats that can be remotely hosted. However, the 
custom tracks utility does not offer the data persistence and track
configurability provided by the track hub mechanism: hub tracks can be 
grouped into composite or super-tracks and configured to display the data 
using a wide variety of options. 
There is no way to create a browser on your own sequence with custom tracks.
In general, for users who have large data 
sets that would be prohibitive to upload, need to ensure the persistence of 
their data, or would like to take full advantage of track functionality, or create a browser on sequence not natively supported by UCSC or a genome browser mirror, 
track hubs are a better solution. 
Both mechanisms give data providers the flexibility to directly add, update, 
and remove data from their display as needed.
</P>
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<!-- ========== What Are Assembly Hubs? ============================== -->
<A NAME="Assembly"></A><BR>

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                            <TR><TD><FONT SIZE="4"><A NAME="TOC"></A><B>&nbsp; What Are Assembly Hubs?</B></FONT>
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                                <p>
				Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted 
				natively on the Browser. Assembly Data Hubs were developed to address the increasing need for 
				researchers to annotate sequence for which UCSC does not provide an annotation database. They allow 
				researchers to include the underlying reference sequence, as well as data tracks that annotate that 
				sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are stored in the 
				same manner as Track Data Hubs. For more information on how to setup your own Assembly Data Hub, please refer
				to the <A HREF="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub wiki</A>. 
				</p>
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<!-- ========== Viewing Hub Tracks in the Browser ==================== -->
<A NAME="View"></A><BR>

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