GenomeView

During the past week a number new features have been implemented, some improvements have been made and a number of bugs have been fixed.

The major addition for this release is a brand new visualization method for multiple alignments.
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The main novelty in GenomeView 773 is the ability to properly display spliced short read alignments. Another feature that is worth mentioning before the list of changes is that you can now reorder the tracks in the track overview panel by dragging them.

Furthermore, there were a lot of improvements 'under the hood' and some polishing fixed to the GUI.

• Improved logging of events for easier crash diagnostics
• Upgraded to the latest version of SAMtools
• Fixed some navigation issues introduced in 687
• Made columns in the information panel unmovable
• Fixed a couple of bugs in the wiggle track
• Improved file type detection

The development of GenomeView is ongoing. Because of the many releases, the version numbering scheme has changed. The version number will from now on correspond to the revision in the Subversion repository.

This release bring a number of improvements which include:

• Improvements to the wiggle-track: fixed color coding, added logarithmic scaling,
• Speed improvements: mainly for short read alignments
• Lower memory footprint allowing more data to be loaded at once
• Added drag'n drop support, you can now drag one or multiple files onto GenomeView and it will be loaded
• Added an option to run a single instance of GenomeView that will handle all invocations instead of starting a new program every time you click a link.
• Fixed a number of bugs
• Added an export function to save high resolution images from the visible data

These sequence of releases focused on improving a number of aspects of GenomeView. First of all support for access to BAM files was added over http, without requiring the whole file to be downloaded. Paired-end reads are now also properly linked together and visual represented as a pair. Editing genes has been made more user friendly and the configurations have been significantly expanded.

List of changes

• Fixed issue with undo-redo queue
• Hover window for short-read coverage
• Display pairing of paired reads
• Bug fixes all around

Release 1.9992 of GenomeView finally provides a way to store sessions and restore them later on. For now the functionality is rather basic and GenomeView only keeps track of what data is loaded and will restore it when loading a session.

The visualization of short read data has been improved. When hovering over the pile-up plot, you get a pop-up showing the actual number of reads. Also a number of additional constraints and checks have been implemented to keep GenomeView alive and responsive when browsing data sets that have extreme high coverage (>10,000 stacking depth) in some places. Furthermore, the pile-up graph is now split in forward and reverse strand coverage.

Download latest version of GenomeView and JAnnot
The preferred way to start GenomeView is the web start you find in the top-left corner of the site.
JAnnot 1.98 API docs

During the past few weeks a lot of features have been added and improved in GenomeView and JAnnot. Most of the intermediate versions have only been made available internally in the SVN, but I think it's time for another public release. There are three notable changes from version 1.90. First the GUI is reorganized to be easier to use. Second, we have added support for short read (RNA-Seq, Chip-Seq, etc.) data Next-generation sequencing can now be visualized with GenomeView. And third, we have added support for authentication and SSL to ensure secure transfer of your data.

Download latest version of GenomeView and JAnnot
The preferred way to launch is still the web start you find in the top-left corner of the site.
JAnnot 1.96 API docs

A non-exhaustive list of improvements, changes and new features that found their way into GenomeView in the past few months is provided in the rest of the announcement.

The latest version of GenomeView has two main new features: support for multiple alignments and the ability to display syntenic blocks

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In the rest of the announcement you find a description of the new features with some screen shots.

JAnnot has now support for a few new data types:

• Wiggle tracks (continuous valued data), with some parsers and an internal representation
• Multiple alignment data, with some parsers and internal representation
• Added support for syntenic block representation

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API docs

JAnnot 1.2 is released. This is the first public release of JAnnot. JAnnot is a Java library to handle biological sequence data. It was developed to handle the data in- and output of GenomeView.

JAnnot is under active development to cater the needs of GenomeView. It is provided as stand-alone library as-is for those interested. At the moment there is little documentation, however this is one of the focus points in the near future.

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API docs

This releases features a major redesign of the plugin architectures that uses the JPF framework more properly and can account for dependencies between the different plugins. Together with this release we have also released two completely new plugins and we have updated the two plugins that were already available. The two new plugins are for NCBI Blast and for SpliceMachine (a splice site prediction program).