Important changes in this major release include:
Shared storage: sharing of bioinformatics data in a lab. For details, see this page - http://ugene.unipro.ru/shared-db.html.
UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
An overview video about the new UGENE version is available here - http://www.youtube.com/watch?v=NlFQNZcE0LU.
More information see here - http://ugene.unipro.ru/