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UGENE video podcast series teaches you to work with UGENE and answers popular users questions.

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#40: What’s new in UGENE 1.13?

Important changes in this major release include:

  • DAS: you can now annotate an unknown amino acid sequence using annotations of its homologs. First, you search for homologs using the Uniprot BLAST. Second, you load the annotations of the selected homologs to your sequence using the Distributed Annotation System (DAS).
  • NCBI Genbank search interface: search for DNA and protein sequences in the GenBank database directly from UGENE.
  • Bowtie2: use sequencing reads aligner "Bowtie2" from UGENE GUI.
  • Codon table: a new help view "Codon table" was added into the Sequence View. Click "Ctrl+T" to open it there.
  • Multiple Alignment Format: a new format PHYLIP is now supported.
  • Assembly Format: ACE format is now opened in the Assembly Browser.
  • NGS pipelines: "Call variant with SAMtools" pipeline was optimized.
  • Workflow Designer:  there were a lot of major and minor improvements.

    • Usage of a common workflow output directory
    • Storing history of a workflow execution (in dashboards)
    • Managing of different workflows output
    • Re-running of a workflow from a dashboard
    • Debugging of a workflow execution and investigation of an intermediate data state.
    • "Workflow schemas" were renamed to "workflows"

#39: What’s new in UGENE 1.12?

The latest UGENE 1.12 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.

Short list of major features:

  • The new entity 'Datasets' in the Workflow Designer which replaces URL parameters
  • The MSA editor has been upgraded with pairwise alignment algorithms and the sequence highlighting
  • The Assembly Browser allows exporting consensus variations in VCF4 and Simple SNP formats
  • Integration with BioMart: extensions for WEB-browsers (Mozilla Firefox and Google Chrome)

#38: What’s new in UGENE 1.11?

The latest UGENE 1.11 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.

Short list of major features:

  • The Sequence View was extended with an options panel
  • A consensus sequence for assembly data in the Assembly Browser was added.
  • New data flow elements Grouper and Multiplexer in the Workflow Designer were added.
  • An mRNA-to-genomic alignment program Spidey was embedded into UGENE as an external tool.
  • UGENE 64-bit version is now available for Windows.

#37: What’s new in UGENE 1.10?

The latest major UGENE 1.10 release introduces a lot of new features, brings stability, performance and usability improvements into UGENE.

Short list of features and improvements:

  • New tools: MrBayes, BWA (all platforms)
  • Update of Bowtie and BLAST tools
  • Short reads assembly viewer: performance and reads coloring improvements
  • Open, view and annotate huge DNA files on a usual desktop
  • Workflow Designer: new data filtering elements
  • Sequence viewer: new DNA Flexibility and GC Frame Plot graphs
  • All in one package: download UGENE, documentation and external tools in a single file

#36: Browsing BAM files with UGENE Assembly Browser

What does the future hold for browsing and analysis of assembly data?

This video shows how to use UGENE Assembly Browser – an innovative and fast tool for working with NGS data.

#1-40: The whole episodes list