What's New in Geneious Prime 2020?

Geneious Prime 2020

Longread sequence mapping with Minimap2 (external plugin)

Fast and easy alignment of Oxford Nanopore and PacBio data to a reference sequence using an industry recommended tool, without the hassle of the command line.

Clustal Omega replaces ClustalW for better, faster alignments

Scale up your alignments with Clustal Omega, now included with Geneious Prime. The HMM alignment engine improves both quality and speed of alignments compared to the older ClustalW aligner.

Better back translate and codon optimization

New codon optimization algorithm lets you match the codon usage from your organism of choice by generating a new sequence, starting from either a protein or nucleotide sequence. Optionally eliminate rare codons and restriction sites.

More accurate annotation of CDS features onto your plasmids

Automatic annotation of plasmids is now smarter with adjustment of CDS boundaries to match the nearest valid ORF when annotating single-interval CDSs from your reference features database.

Add your favorite tools to Geneious with improved Wrapper Plugin system

Can’t wait for us to add your favorite command line aligner, tree builder or assembler? You might be able to add it yourself from right inside Geneious using the Wrapper Plugin Creator plugin. Coding skills are not required, though a good understanding of command line interfaces and file formats is.

Many other small improvements

  • Share Text View settings with your team for consistent formatting
  • Easily check for stop codons in the Sequence View with a new color scheme
  • Show the folder path as ‘breadcrumbs’ for easy navigation
  • Take advantage of new primer characteristics including calculation of Tm on longer sequences
  • And more….

Want more details?

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

What Was Added in Previous Versions?

Geneious Prime 2019

Rapid Manual Primer Design
Select desired binding site in the Sequence View to see real-time display of length and melting point (Tm) then easily add a primer annotation with a convenient new button.
Powerful Primer Annotation Display
5′ extensions (tails) on annotated primers are now displayed inside the sequence view to indicate the length of the extension, the nucleotides it contains and what functional elements are present such as restriction sites, spacers and tags.
Simplified Testing and Annotation of Existing Primers
Easily search all folders for primers that match a sequence of interest with the redesigned “Test with Saved Primers” operation. Copy and paste primers from other programs into the new “Add Primers” operation to find them on your target sequence in one step.
Drag and Drop Sequence Export
Export annotated sequences in GenBank format by simply dragging documents out of Geneious Prime and onto the desktop or into another program.
Easy Extraction of PCR and Restriction Digest Products
Shift click between two compatible primers or restriction enzymes for quick and easy extraction of their product from your sequence.
Improved Protein Statistics
Calculate on the fly statistics for protein sequences directly on nucleotide sequences within the Statistics panel
Improved GenBank Export
Export the information you need with your sequences using the simplified, flexible options to include your own Meta-Data fields and allow or constrain export parameters to suit downstream applications.
Publish Plugins via Internal Network
Create a curated list of plugins to offer privately to members of your organization via your internal network.
Customizable Text View – Sequence Layout 
Format to alter wrapping, numbering, sequence color and presence of reverse complement and translation
Customizable Text View – Alignment Layout
Format to alter numbering, sequence color and highlighting of agreements/disagreements to consensus
Customizable Text View – GenBank Format
GenBank format available for all individual sequences
Primer Specificity
Primer specificity automatically tested within the template sequence when designing primers, and presence of any additional binding sites recorded on the primer annotation
Primer Design Improvements
Option to control the minimum distance between primers designed on the same strand – defaults to minimizing creation of duplicate primers when multiple primer pairs are designed together
Annealed Oligo Cloning
Added workflow to create a sequence with annotated overhangs representing the sticky ends created by annealing two partially overlapping oligos
Sanger Sequencing Primer Design
Quickly design primers for Sanger sequencing of vectors, inserts or other sequences
Vector NTI Database Import
Easily import your complete Vector NTI database with simple drag and drop, for both Vector NTI Express and Advance databases.
Improved Text View Formatting of Sequences and Alignments
Support formatting and export of sequences in accordance with U.S. Patent Office requirements as well as other improvements.
Primer Characteristics
Quick and easy primer pairing in the Sequence View to link two primers of your choice and calculate pair dimer Tm and product size.
Easier Shared Database Rollout
Immediately access shared data and get straight to doing your research with a Geneious Shared database connections now able to be pre-configured by your IT team or admin when rolling out a version of Geneious Prime. Includes improved support for Windows authentication.

Geneious R11

Parrot
Volcano Plots for RNA-Seq Expression Analysis
Visualize gene expression in an interactive volcano plot that can be used to highlight and jump to differentially expressed genes.
Pretty PCA Plots
Create beautiful PCA plots with better labelling and new visualization options.
Silent Mutation Analysis for Restriction Sites
Automatically identify point mutations in a coding sequence that will introduce a restriction site without affecting the protein.
CRISPR Cpf1 Option
Added support for CRISPR-Cpf1 with a 5’ PAM site. Find sites in A and T rich sequences and with higher cleaving efficiency in vivo.
Create Enzyme Sets
What’s in the freezer? No longer pull information from other sources. Now you can easily create your own enzyme sets.
Better FASTQ Import
Paired reads can be associated with each other during import and Geneious will do it’s best to guess how they’re paired. Read technology can also be set.
Updated Mauve Plugin for Bacterial Genome Alignment
Now includes support for sequence lists and the MCM operation for reordering contigs, making it possible to align draft genomes and perform genome finishing.
CRISPR-Cpf1 Specificity Scoring
Confidently pick the best CRISPR-cpf1 guide RNA sites using a new specificity score which is calculated from an off-target analysis against your database of choice.
Smart NGS Import
Drop any assortment of SAM, BAM, GFF, BED, and VCF files into Geneious to import in one easy step, even if you have a mixture of different samples and reference sequences.
Better BLAST Server Management
Set up several BLAST server mirrors at once and choose the best one each time you do a search. No more switching mirrors each time.
NCBI BLAST Cloud Support
It’s never been easier to set up your own BLAST mirror thanks to NCBI BLAST Cloud. If you set up a mirror in this way, Geneious can now connect to it natively.
Concatenate by Index
Concatenate sequence lists and alignments by index, rather than by name, which is super useful for merging paired reads that don’t quite overlap.
CSV/TSV Export of Sequence Lists
Export all of the sequences in a sequence list along with their metadata to CSV or TSV so you can drop them in Excel or similar for further analysis.

Geneious R10

Bee
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
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
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
Zip files containing multiple files and sub-folders can now be imported
Sequence Viewer
Added ‘Copy Translation’ to translate selected regions of a nucleotide sequence (in right-click menu)
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)
Find CRISPR Sites
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
RNA-Seq Expression Analysis
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
Restriction Cloning, Gibson Assembly and Golden Gate can now be incorporated into Workflows. Automate your cloning procedures or perform high-throughput batch cloning.