Geneious Prime for Mac

Features

• Add short sequences like spacers or tags when simulating Gibson and In-Fusion cloning (Academic/Enterprise only)
  • Optionally add Upstream and / or Downstream bases to Insert sequences
  • Construct spacer sequences from choice of bases, enzymes, Gateway sites or sequences from your Geneious database
  • Spacers are incorporated into designed primers or concatenated onto sequences for synthesis, and accounted for when designing overlap regions
• CRISPR on-target scoring now supports Doench et al (2022) algorithm, that takes tracrRNA variants into account
• New Synthesise Inserts option for Golden Gate Cloning enables automatically adding the appropriate enzyme and overhangs to Inserts sequences for ordering
• Parts Cloning Enhancements
  • Now accepts circular backbone vectors, which can be linearized by selecting a point to cut at, or one or more annotations or intervals to excise
  • One-step multiple insertion point Parts cloning, enabling the insertion of non-contiguous fragments into a circular vector backbone (Academic/Enterprise only)
  • Restructured the UI to provide a more natural flow

Minor Features and Usability Improvements

• Breadcrumbs: Clicking on the name of a folder which is already selected now scrolls to it in the folders list
• Gibson and In-Fusion cloning run via the CLI now supports digestion of a circular backbone for Single Insertion Point cloning
• Improved Cloud Workspace performance
• The Flye plugin has been updated to version 2.9.6 of Flye, and now supports Ubuntu 24
• Shared Database: Added option to choose SSL security settings when creating a new connection of type MySQL or MS SQL
• Maximum memory used by Prime on Windows can now be changed without requiring administrator permission

Fixes and Minor Changes

• Merge Paired Reads: Fixed so that when run on multiple data sets, if one set fails to merge the other sets are still merged
• Fixed an issue whereby cloning operations would run via the CLI when an error was present in the option parameters
• Fixed a bug where cloning reports did not link to results after changing the original input documents
• Document Table: Fixed rare bug where the name column was vertically scrolled independently of other columns sometimes
• Fixed bug which caused some CRISPR scoring results for Doench et al (2014) to be undefined
• Fixed the Geneious Server Database installation script link for downloading tomcat
• Fixed a bug where minimap would fail to complete on some reads
• SnapGene Import: Fixed a bug introduced in 2026.0 which caused Geneious to fail to import some SnapGene files
• Fixed a bug where cloning could not be performed with certain combinations of sequences downloaded from Luma
• Fixed an issue which prevented the sample Genomes from being able to be downloaded
• Fixed an Out of Memory error which occured sometimes when grouping large sequence lists together
• Fixed invalid activation issue that could occur when running the Geneious Prime desktop application and command line interface simultaneously
• Fixed problem where Name column width would reduce to a maximum of 500 pixels wide when editing names or switching the viewed folder
• Fixed a bug which caused a hang during shutdown when accessing a large Microsoft SQL server shared database
• Restored AppNap support for older macOS systems
• Updated SamImporter htsjdk library to v3.0.5
• Cloud workspace: Added a warning when copying annotator results to local workspace
• Cloud workspace: Improved the loading speed of the document lineage view
• Fixed a bug which prevented activation of email Sign in licenses when using a docking station on Linux
• Fixed a bug where cloud documents that were search results would remain in memory even after they were deleted under certain conditions
• Fixed an issue where the Cloud disk cache was not updated with additional XML in some circumstances, leading to loss of Sequence Viewer settings and selection.
• Cloud workspace: Fixed an error updating lineage when many documents were deleted in bulk
• Cloud workspace: Fixed an issue where you might be unexpectedly logged out from Geneious Cloud after your computer was sleeping or briefly disconnected from the internet
• Cloud workspace: Fixed bug where deleted folders remained displayed in Favorites
• Cloud workspace: Fixed bug which resulted in the wrong options being presented in the Geneious Cloud folder sharing dialog
• Cloud workspace: Fixed potential crash when updating large quantities of Geneious Cloud documents
• Cloud workspace: Fixed some occasional cases where an empty folder would display a download complete label
• Cloud workspace: Improved performance in Geneious Prime when responding to restoration of deleted documents from the web
• Cloud workspace: Should now display a more clear warning when the workspace is in read-only mode due to an expired subscription
• Cloud workspace: Tidied up folder sharing dialog
• Fixed a bug where a dialog warning about read-only could pop up shortly after deleting the results of a recent operation
• Cloud workspace: Fixed a crash that occured rarely when logging out with websockets active
• Cloud workspace: Fixed a rare crash that would occasionally occur when deleting folders
• Cloud workspace: Fixed a rare crash when logging out
• Cloud workspace: Fixed a very rare crash that would occasionally occur when logging out of Cloud
• Cloud workspace: Improved the handling of document creation requests in organizations that are over their storage limit
• Fixed a bug that could occur when selecting a large number of documents on the cloud and then performing Batch Rename before they finished loading
• Star Assembler: Fixed a bug where it could not be run on documents with unusual characters in their names
• Fixed bug causing some CRISPR scoring results for Doench et al. (2014) to be undefined
• Interproscan: Fixed issue that caused Interproscan searches to fail
• Fixed various bugs in selecting range/annotations
• Fixed bug in beta where Circular Product option is not disabled when circular backbone is chosen in Parts cloning
• SnapGene Import: Fixed failure to import some files which had manual edits made between a PCR step and a cloning step
• Fixed a crash which could occur in the beta version when linearizing a circular backbone sequence of zero length
• Luma: Fixed a bug where nucleotide sequence regions did not have attached antibody IDs