During the Workshop on next generation sequencing data analysis, June 1-4, Espoo, FinlandGenomeView will be covered during a hand-on session and during the conference day.
The information for the practical session is available online.
There are two new visual features in GenomeView:
1) Short read alignments contain now visual clues to the read alignment quality. Reads with a high mapping quality are colored dark, while reads with low mapping quality will be lighter.
2) At the top of the short read track there is now also a SNP track shows the frequency of alternative nucleotides for a position.
3) Major improvements to the visualization of the gene structure track to make it look a lot less clunky.
4) Uniform mouse-functions throughout the visualization tracks.
GenomeView 894 is a maintenance release, fixing a number of bugs in both JAnnot and GenomeView. No stunning new features have been implemented.
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.
Watch video full screen in HD mode for best quality, the video contains no sound
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.
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:
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
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.
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.