UGENE

UGENE
Developer(s) Unipro
Stable release 1.22.0 / 6 April 2016 (2016-04-06)
Written in C++, Qt
Operating system Cross-platform
Available in English, Russian
Type Bioinformatics toolkit
License GPL
Website ugene.net

UGENE is free open-source bioinformatics software.[1][2] It works on a desktop computer with Windows, Mac OS X or Linux.

UGENE helps biologists to analyze various biological data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g. a lab database).

UGENE integrates dozens of well-known biological tools and algorithms, as well as original tools in context of genomics, evolutionary biology, virology and other branches of life science. UGENE provides a graphical interface for the pre-built tools so biologists without programming skills can access those tools more easily.

Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks executing embedded tools/algorithms and data writers. Blocks can be created with command line tools or a script. A set of sample workflows is available in the Workflow Designer (for annotating sequences, conversion of data formats, NGS data analysis, etc.)

Besides the graphical interface, UGENE also provides a command-line interface. A workflow made by the Workflow Designer can be executed using the command-line interface.

In order to provide better performance, UGENE utilizes multicore CPUs and GPUs to optimize a few algorithms.[3][4]

Key features

The software supports the following features:

Sequence View

The Sequence View is used to visualize, analyze and modify nucleic acid or protein sequences. Depending on the sequence type and the options selected, the following views can be present in the Sequence View window:

Alignment Editor

The Alignment Editor allows working with multiple nucleic acid or protein sequences - aligning them, editing the alignment, analyzing it, storing the consensus sequence, building a phylogenetic tree and so on.

Phylogenetic Tree Viewer

The Phylogenetic Tree Viewer helps to visualize and edit phylogenetic trees. It is possible to synchronize a tree with the corresponding multiple alignment used to build the tree.

Assembly Browser

Assembly Browser

Assembly Browser project was started in 2010 as an entry for Illumina iDEA Challenge 2011. The Assembly Browser allows a user to visualize and browse large (up to hundreds of millions of short reads) next generation sequence assemblies. It supports SAM, BAM (which is the binary version of SAM) and ACE formats. Before browsing assembly data in UGENE, an input file is converted to a UGENE database file automatically. This approach has its pros and cons. The cons are that the conversion may take time for a large file and there should be enough disk space to store the database. On the other hand, this allows to view the whole assembly, navigate in it and go to well-covered regions rather rapidly.

Workflow Designer

UGENE Workflow Designer allows creating and running complex computational workflow schemas.[6]

The distinguishing feature of the UGENE Workflow Designer in comparison with other bioinformatics workflow management systems is that workflows in UGENE are executed on a local computer. It helps to avoid data transfer issues, whereas other tools’ reliance on remote file storage and internet connectivity does not.

The elements that a workflow consists of correspond to the bulk of algorithms integrated into UGENE. Using the Workflow Designer one can also create custom workflow elements. The elements can be based on a command-line tool or a script.

Workflows are stored in a special text format. This allows transferring the workflows to other users and reusing them.

A workflow can be run using the graphical interface or launched from the command line. The graphical interface additionally allows controlling the workflow execution, storing the parameters, and so on.

There is an embedded library of workflow samples for converting, filtering and annotating of data. Particularly, there are several pipelines for analysis of NGS data developed in collaboration with NIH NIAID. A wizard is available for each workflow sample.

Supported biological data formats

Release cycle

UGENE is primarily developed by Unipro LLC with headquarters in Akademgorodok of Novosibirsk, Russia. Each iteration lasts about 1–2 months, followed by a new release comes out. One can also download a development snapshot of the software.

The features to be included in each release are mostly initiated by users.

See also

Related software

References

  1. ↑ Okonechnikov, K.; Golosova, O.; Fursov, M.; the UGENE team (2012). "Unipro UGENE: a unified bioinformatics toolkit". Bioinformatics 28 (8): 1166–7. doi:10.1093/bioinformatics/bts091. PMID 22368248. Cite uses deprecated parameter |coauthors= (help)
  2. ↑ Fursov, M.; Novikova, O. (2008). "Multitasking software system for DNA analysis" (PDF). Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure 1: 78. ISBN 978-5-91291-005-0.
  3. ↑ Fursov, M. Y.; Oshchepkov, D. Y; Novikova, O. S. (2009). "UGENE: interactive computational schemes for genome analysis" (PDF). Proceedings of the Fifth Moscow International Congress on Biotechnology 3: 14–15. ISBN 5-7237-0372-2.
  4. ↑ Efremov, I. E.; Fursov, M. Y; Danilova, Yu. E. (2009). "UGENE: high performance genome analysis suite". Proceedings of the Fifth Moscow International Congress on Biotechnology 2: 405–406. ISBN 5-7237-0372-2.
  5. ↑ Vaskin, Y.; Khomicheva, I.; Ignatieva, E.; Vityaev, E. (2012). "ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes". In Silico Biology 11 (3-4): 97–108. doi:10.3233/ISB-2012-0448. PMID 22935964.
  6. ↑ Fursov, M. Y.; Varlamov, A. (2009). "UGENE - A practical approach for complex computational analysis in molecular biology" (PDF). Proceedings of the 10th Annual Bioinformatics Open Source Conference: 7.

External links

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