SUMMARY: UGENE is a free, open-source, cross-platform bioinformatics software. UGENE deploys pre-defined pipelines and a flexible instrument to design new workflows and visually build multi-step analytics pipelines. The new UGENE v.1.31 release offers graphical, user-friendly wrapping of a number of popular command-line metagenomics classification programs (Kraken, CLARK, DIAMOND), combinable serially and in parallel through the workflow designer, with multiple, customizable reference databases. Ensemble classification voting is available through the WEVOTE algorithm, with augmented output in the form of detailed table reports. Pre-built workflows (which include all steps from data cleaning to summaries) are included with the installation and a tutorial is available on the UGENE website. Further expansion with multiple visualization tools for reports is planned. AVAILABILITY AND IMPLEMENTATION: UGENE is available at http://ugene.net/, implemented in C++ and Qt, and released under GNU General Public License (GPL) version 2.

UNLABELLED: Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. AVAILABILITY AND IMPLEMENTATION: UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.