What's New in Geneious R10.2?

Download R10.2

6 June 2017
The second Geneious R10 update is here. R10.2 is free if you have a valid subscription or a perpetual version R10 license. If you are currently using a previous version-only licence (eg R9), you will have to purchase an upgrade.

RNA-Seq Expression Analysis (R10.2)

Compare Expression Levels now has the option to use DESeq2 for pairwise analysis with replicate samples and will produce a principle component analysis (PCA) plot for quality control.

Cloning Workflows (R10.2)

Restriction Cloning, Gibson Assembly and Golden Gate can now be incorporated into Workflows. Automate your cloning procedures or perform high-throughput batch cloning.

Smarter Restriction Cloning

Completely redesigned to be much simpler and more powerful. Includes automatic identification of compatible cut sites, and digestion and ligation with drag and drop ordering of fragments.

Alignment Masking

Mask unreliable alignment sites for better tree building, without deleting data. Manage alignment masking patterns using annotation tracks and automatically mask sites according to user defined criteria.

Improved Plasmid Viewer

The new circular overview option helps you stay oriented by showing the bases of the sequence and the plasmid map alongside each other with synchronized editing, selection and scrolling.

Chimera Filtering

Filter chimeric reads by comparing to a reference database, which can be any sequence list or alignment. Choose between the bundled public domain UCHIME algorithm or the faster USEARCH implementation.

Lineage View for Parent/Descendants

Lineage View is now easier to access as a separate tab and details about your cloning operations are shown right next to the relationships.

Assembly and Mapping

Better structural variant mapping, a new workflow to build SNP trees by applying variants to a reference and better de novo assembly of Ion Torrent, 454, and PacBio CCS data.

Improved Cloning (R10.1)

Gibson and Golden Gate now has sequence view of fragments within the options. Gibson assembly can now saves primers for easy ordering

Annotate from Database (R10.1)

Annotate nucleotide sequences from a protein database by comparing translations of the nucleotide sequence in all six frames with the protein database sequences

Zip Import (R10.1)

Zip files containing multiple files and sub-folders can now be imported

Sequence Viewer (R10.1)

Added ‘Copy Translation’ to translate selected regions of a nucleotide sequence (in right-click menu)

SPAdes de novo assembler (R10.1)

For MacOS/Linux: 64 bit OS is required. For Windows, 64 bit Windows 10 (with recent updates installed) is required. You also need to install additional Windows features (Instructions)

Find CRISPR Sites (R10.1)

  • Major performance improvements were made to the off-target scoring algorithm
  • All CRISPR sites will now be scored against all potential off-target sites in every run
  • Scoring CRISPR sites against off-targets now takes a seed region into account. This is a 10 bp region adjacent to the PAM site that can tolerate a maximum of 2 mismatches and 0 indels

New Core Features of Geneious R10

Cloning

  • UPDATE Gibson Assembly: Can now save the primers used
  • UPDATE Gibson and Golden Gate: Now has sequence view of fragments within the options
  • Restriction Cloning: Completely redesigned to be much simpler and more powerful
  • Restriction Cloning: Automatic identification of compatible cut sites from any number of annotated or unannotated enzymes
  • Restriction Cloning: Manual controls for choice of cut site and treatment of sticky ends such as blunting and filling
  • Restriction Cloning: Digest and ligate any number of sequences in one step with drag and drop ordering of fragments
  • Restriction Cloning: Embedded sequence view shows target region for each fragment

RNA-Seq

  • UPDATE RNA-Seq expression analysis: Compare Expression Levels now has option to use DESeq2 for pairwise analysis with replicate samples

CRISPR

  • UPDATE Find CRISPR Sites:
    • Major performance improvements were made to the off-target scoring algorithm
    • Speed and Filter strategies were removed because off-target scoring is no longer a rate-limiting step. This means all CRISPR sites will now be scored against all potential off-target sites in every run
    • Scoring CRISPR sites against off-targets now takes a seed region into account. This is a 10 bp region adjacent to the PAM site that can tolerate a maximum of 2 mismatches and 0 indels

Assembly

  • UPDATE SPAdes de novo assembler: For MacOS/Linux: 64 bit OS is required. For Windows, 64 bit Windows 10 (with recent updates installed) is required. You also need to install additional Windows features (Instructions)
  • Structural Variant Mapping: Adding support for insertion discovery when the ends of a read map to nearby locations but the center of the read doesn’t map
  • De Novo Assembly: Better results when assembling Ion Torrent, 454, and PacBio CCS data
  • Map to Reference: Better results when mapping Ion Torrent, 454, PacBio CCS and PacBio CLR data
  • Map to Reference and De Novo Assembly: Faster on long reads (e.g. PacBio)

Sequence/Alignment/Contig View

  • UPDATE Sequence Viewer: Added ‘Copy Translation’ to translate selected regions of a nucleotide sequence (in right-click menu)
  • UPDATE Annotate from Database: Will annotate nucleotide sequences from a protein database by comparing translations of the nucleotide sequence in all six frames with the protein database sequences
  • Circular Overview: Added a setting to show a zoomed out overview of circular sequences
  • Total number of non-gap nucleotides or amino acids now shown in Statistics tab
  • Three letter amino acid codes can now be shown by zooming in to 200% on protein sequences or by turning on ‘Three letter amino acids’ in the translation controls for nucleotide sequences
  • Sequences that contain a selection or have the cursor in them are highlighted with a different background color
  • Go To Base now allows selection of region that crosses the origin for circular sequences
  • Shortcut key added for editing the selected sequence’s name or other displayed field (default F2)
  • Scroll past the origin of circular sequences using scroll wheel, panning or left/right arrow keys

Alignment Masking

  • Mask alignment sites that should be excluded when tree building by adding a Masked annotation to the consensus instead of deleting the site completely
  • Choose whether or not to exclude masked sites when running any of the tree builders available for Geneious
  • Choose whether to gray-out or completely hide masked sites in the Alignment View
  • Automatically mask sites according to various criteria using ‘Mask Alignment’ in the Tools menu (previously called ‘Strip Alignment Columns’)
  • Store multiple alternative masking patterns on the same multiple alignment using annotation tracks
  • Import masks from the EXSETs defined in the ASSUMPTIONS block of NEXUS files
  • New option to mask or strip sites according to user-defined ranges of sites, or strings of 0’s and 1’s using ‘Mask Alignment’ in the Tools menu
  • Mask Alignment now ignores trimmed regions of sequences when determining if a site contains ambiguous states
  • Mask Alignment now ignores end gaps when computing the percentage of gaps (for contig alignments only)
  • Mask Alignment now ignores gaps when determining if a site contains all identical nucleotides/amino acids

Chimera Filtering

  • Filter chimeric reads from sequencing data by comparing to a reference database using ‘Remove Chimeric Reads’ in the Sequence menu
  • Choose between the bundled public domain UCHIME algorithm or the faster USEARCH implementation (USEARCH must be downloaded separately)
  • Use any sequence list or alignment as the reference database, links and instructions for importing suggested databases are included

Parent/Descendant Improvements

  • Lineage View is now easier to access as a separate tab
  • View the options used when an operation was run by clicking ‘Show Options’ in the Lineage View (for supported cloning operations only)
  • Even more information about operations is now shown in the Lineage View
  • The region of sequences used in an operation is now shown next to each sequence in the Lineage View
  • ‘Go to’ in the Lineage View now selects the region of a sequence that was used

General

  • UPDATE Import: Zip files containing multiple files and sub-folders can now be imported
  • Clone Manager Import for molecule files (.cm5)
  • Text Document creation and editing – Create a blank text document via File > New and edit plain text documents inside Geneious
  • Variant Finding / SNP Trees: Added a workflow to apply discovered variants to the reference sequence in order to create a variant sequence. This is useful for the creation of SNP trees
  • New Sequence: Added the ability to specify a binding region to simplify entering primers or probes that have extensions
  • Cloning: Create active parent/descendant links when pasting a sequence using ‘Paste with Active Link’ in the right-click menu of the Sequence View
  • Aliases: Store a single document in multiple folders simultaneously using ‘Paste Alias’ in the Edit menu or by holding Ctrl+Shift when dragging (Cmd+Alt on macOS)
  • Folder Search: Find folders by name in the Sources Panel by typing a keyword and pressing Enter

Want more details?

All updates including minor changes and bug fixes can be viewed in the full Geneious release notes