Introducing Savant: Genome Browser for HTS Datasets

[mfiume]

We are excited to announce the release of Savant, the Sequence Annotation Visualization and ANalysis Tool, a new genome browser which combines visualization of HTS and other genome-based data with powerful analytic tools. Savant is designed to be easy to use, to support files of various formats and sizes, to be fast and memory efficient, and most importantly, to be extensible. Savant has a bookmarking component that allows users to quickly navigate among regions of interest, a Table View that provides a textual view of the visualized data, and novel visualization modes that make the interpretation of genomic information (e.g. paired-end relationships) easier. Finally, the plugin framework of Savant exposes a rich library of functions (e.g. for retrieving data, setting the range, manipulating the UI) which developers can use to create, for example, custom on-the-fly computational analyses. Plugins can be shared through the Savant website, creating an environment through which developers can deploy analytic tools and users can create customized workflows.

For more information and to download Savant, visit http://compbio.cs.toronto.edu/savant/.

If you need any help with Savant, please contact the Development Team by email to savant [at] cs [dot] toronto [dot] edu.

- Marc Fiume

[mfiume]

We are happy to announce the release of a new and substantially improved version of Savant. Since the previous post, many great features have been added, including:

• multi-chromosome support
• better formatting stability
• vertical panning for high coverage read alignments
• new visualization modes
• SNP finder plugin
• much more!

Download Savant here: http://compbio.cs.toronto.edu/savant/

A manuscript describing Savant has been published in Bioinformatics, linked here: http://bioinformatics.oxfordjournals.../16/1938?rss=1

[mfiume]

Savant v1.3.2 Released

We have just rolled out another release of a Savant. New display modes have been added, including a really useful SNP mode! Many file formatting quirks have been worked out as well. Thanks for all your questions and thanks for using Savant!

Download Savant here: http://compbio.cs.toronto.edu/savant/

[mfiume]

Version 1.4.1 Release Announcement

The Savant Dev Team has just released v1.4.1, which includes lots of exciting new features:

• Visualization of remote tracks (http, ftp)
• 1000 Genomes Alignments Plugin
• Support for sessions
• Stand-alone data formatter
• Greatly increased speeds for coverage / continuous files
• Many UI improvements

Savant has a new home: http://www.savantbrowser.com/.

[mfiume]

Savant version 1.4.4 released!

Greetings Seq Community,

We just released a new version of Savant, with many new features, bugfixes, and plugins. Among the many additions, we're most excited to announce our new UCSC Plugin, which provides a familiar interface for users to add almost every UCSC track directly into Savant!



You can download the latest version at http://genomesavant.com/.

- Marc

[tarkvara]

Savant 1.5.1 released

The Savant development team would like to announce the release of version 1.5.1 of the Savant genome browser, with many new features, bug-fixes, and plugins. A full list of changes can be found at http://www.savantbrowser.com/release.html. Highlights include:

• Support for accessing tracks over https
• UCSC plugin provides access to most tracks from the UCSC Genome Browser (now including Wig tracks)
• Searching by gene or feature name (for both local and UCSC tracks)
• Display of cytoband information
• Improved display of coding regions
• Built-in genomes for commonly-used organisms
• Strand SNP visualisation mode
• Support for TDF and Tabix data formats
• Autoupdate of plugins
• New WikiPathways plugin
• New Cufflinks plugin

You can download the latest version at http://savantbrowser.com.

Eric Smith
Savant Development Team