In your methods section, please cite “Geneious version (the version you are using) (http://www.geneious.com, Kearse et al., 2012)”
And cite the paper below in your reference list:
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Mentjies, P., & Drummond, A. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.Bioinformatics, 28(12), 1647-1649.
You can export graphics from Geneious using File→Save As Image File…. If you are exporting the file in .jpg or .png format the default resolution is quite low, so you should increase this to about 400% to make the image look good when printed. JPG and PNG images are made up of dots so don’t scale well. For scaleable graphics, PDF or EPS are good choices. SVG is also scaleable and has the ability to be edited in tools such as Adobe Illustrator or Inkscape. EMF can be edited on Windows using PowerPoint, or LibreOffice Draw on Mac or Linux (the Mac version of PowerPoint can’t modify EMF files). Using SVG or EMF will allow users to tweak the graphic, and add annotations and still have the image scale nicely because it is a vector graphic.
The manual for the latest version of Geneious can be downloaded from here.
The manual is also available for download from within Geneious. Go to Help→Online Resources→Download Manual and you’ll get the current manual for your version of Geneious.
There are tutorials and help sections accessible from within Geneious to give tips and information on all of the different options and features. Access to the manual and contact with support are also available in Geneious.
The Geneious Support Site contains forums, a knowledge base and access to our support scientists for you to browse previously asked queries, communicate with other Geneious users and ask any questions you may have.
Licensing and Purchasing
A personal license is designed for individual use. Geneious can be activated on a maximum of three machines, but will only run on one machine at a time.
A floating license is best for groups that are sharing resources. The number of floating licenses purchased equals the maximum number of simultaneous users. The best package will depend on your group’s usage requirements.
Support consists of both scientific and technical support and can be accessed directly via Geneious or by visiting the support website. All support services are undertaken by highly qualified staff with deep domain expertise.
Scientific support gives you greater understanding of functionality and how to work with Geneious to achieve your goals. From basic functions such as importing sequence data and calling bases, through to more applied activities such as NGS data analysis, constructing phylogenetic trees or designing primers, we have scientific experts available to guide you.
Technical support is for technology related issues that affect your use of Geneious. For example, we actively monitor changes to supported operating systems and external databases such as NCBI and issue updates to Geneious if required. We will also review any specific issues you experience and offer our perspective on how best to address the matter, which occasionally results in a change to Geneious itself.
Geneious reverts back to restricted mode when the subscription has expired. You will receive a reminder before the expiration date. In restricted mode you can view your data and import and export your files, however most other functions are disabled.
If you are on a version-based license plan, a new version upgrade can be purchased at 50% of the current version-only price or you can switch to a subscription based licensing plan. Visit the Upgrade Geneious page to upgrade your license.
Yes, both the student licenses and the trial license allow you to use the full functionality of Geneious.
Yes. Email a purchase order from your university or company, with the intended licensee’s name and email address, to email@example.com, or fax it to +64 9 379 5063. A US$25 handling fee applies. Alternatively, you can request a proforma invoice.
You can renew your subscription easily online up to 60 days before your current license expires:
- Select the license plan you want to purchase
- On the Billing Information page check the “Is this a subscription renewal?’ box
- Enter the start date for your new subscription (the day after your current expiry date)
- Fill in the rest of your payment details
- You will receive your new license key via email
- Enter the license key into Geneious and continue working with no disruption
Installation and System Requirements
This depends greatly on the type of work you will be using Geneious for, but we recommend at least the following:
- Operating System: See below
- Processor: Intel x86/x86_64
- Memory: 2048MB or more.
- Hard-disk: 2GB or more of free space.
- Video: 1024×768 resolution or higher.
Working with NGS data generally requires higher than the minimum system specifications. For optimal performance, we recommend using a Solid State Drive (SSD) and multiple core processor. RAM requirements depend on the type of assembly you are doing, the size of your dataset and genome, and the quality of your data.
The Geneious de novo assembler is intended for use with bacterial genomes and small eukaryote genomes. For assembly of a typical bacterial genome at 100x coverage, a machine with 16 GB of RAM should be sufficient. For more detailed information on RAM requirements for de novo assembly, see here.
Reference assembly (map to reference) is generally less computationally intensive than de novo assembly and can be performed on genomes of any size. Mapping to a bacterial genome typically requires less than 1 GB of RAM; for mapping to the human genome, we would recommend 32 GB of RAM.
Windows 7, 8, 8.1, and 10
Supported Mac operating systems vary depending on the version of Geneious you are running, as follows:
Geneious R10: MacOS 10.8 – 10.12
Geneious R9: MacOS 10.6 – 10.12. Users on OS 10.6 will need to install Java 6 from https://support.apple.com/kb/dl1573
Latest two released versions: currently CentOS 6/7, RHEL 6/7, or Ubuntu Desktop LTS (14.04 and 16.04). Note: 32-bit Linux is not supported for Geneious R10 and above. To run Geneious on Linux you also need the default desktop environment and all packages up to date with latest versions from the distribution repositories.
Yes. A Geneious license is not specific to an operating system and can be used on different operating systems. Download and the install the appropriate version of Geneious for your operating system from our website and activate your license in Geneious.
Geneious databases are stored separately from the application itself, in a folder called Geneious X.Y Data on Windows and Mac or .geneious X.Y data on Linux (where X.Y is the version of Geneious such as 9.0). This is located in the user’s home directory by default (e.g. /Users/yourname/Geneious 9.0 Data).
It is not possible to import .spf files into Geneious as this is a proprietary data format. However, you can export your Sequencher contigs as .caf files and import them that way. If you import the .scf files (chromatogram) files at the same time you should also retain your chromatograms.
You can import a Vector NTI database into Geneious with File->Import->Vector NTI Database. You can also import individual sequences from Vector NTI using File->Import->From File and select Vector NTI as the sequence format.
If you have an Excel file with multiple sequences with name in column A and sequence data in column B you can export from Excel as CSV and then use the Geneious CSV importer.
If you have them in a spreadsheet, the best option is to export from Excel as a CSV file and then use the Geneious CSV importer.
Geneious can import files from Sanger (.ab1 or .scf format) and next-generation (NGS) sequence platforms (fastq or fastq.gz format). The Geneious assembler can handle reads of any length, and works optimally with Sanger, Illumina, Ion Torrent, 454, and PacBio CCS data. PacBio CLR and Oxford Nanopore data is more problematic for Geneious due to the very high error rates. Depending on the data quality, you may be able to use these with map to reference, but are unlikely to be able to successfully de novo assemble them. Hybrid assemblies using a mixture of read types and lengths are also possible.
The Geneious mapper has an RNA-seq setting that can map RNA-Seq reads to a genomic reference sequence. It can discover novel introns and map ends of reads correctly around these novel introns, or it can map reads to introns via CDS, mRNA or junction annotations on your reference sequence. This assembler will also discover fusion genes. Geneious also has a plugin for the Tophat RNA-seq mapper, which works with Geneious versions 7.0 and above.
Geneious also contains tools for digital gene expression analysis, allowing you to calculate normalized expression measures TPM, RPKM and FPKM on reference mappings of individual samples, and to compare values between two samples to find differentially expressed genes. Geneious also implements the popular R package DESeq2 for comparing expression between two sample conditions with replicates. Results are displayed as a heat map annotation track on the reference sequence, and as Volcano and PCA plots.
Yes, Geneious has a full suite of tools for processing amplicon (e.g. 16S) sequences, including quality trimming and chimera removal. The Geneious de novo assembler can be used to cluster reads into OTUs. Tools available for classifying and further analysing sequences include multiple alignment, phylogenetic tree building, BLAST and the Sequence Classifier plugin. Geneious also has a cloud-based 16S biodiversity tool for taxonomic classification of 16S reads against the RDP database.