Geneious Server

Geneious Server is a software package that extends the capability of Geneious Prime to take advantage of your existing enterprise level infrastructure.

Server grade performance for your whole team

Make it easy for biologists to shift computation from the desktop onto HPC resources and enhance your productivity by removing analysis bottlenecks. One click in Geneious Prime and your job runs on the server.

Offload and organize your data

Ensure all of your valuable research data is safe and easily accessible. Results are automatically stored in a central SQL database where researchers can collaborate on it and you can manage data security.

Do BLAST your way

BLAST+ comes built in and its easy to create in-house databases and run searches on them from Geneious Prime, no work required from system administrators.

Supported Algorithms

De novo AssemblyReference MappingMultiple AlignmentPhylogenetic AnalysisOther
Geneious AssemblerGeneious MapperGeneious AlignerGeneious Tree BuilderMerge Paired Reads Using BBMerge
VelvetGeneious for RNAseqClustalWMrBayesRemove Duplicate Reads Using BBTools
Velvet OptimizerMaqMUSCLEPhyMLTrim Using BBDuk
MIRABowtie/Bowtie 2MAFFTPAUP*Remove Chimeric Reads
TadpoleBWAMAUVEConsensus Tree BuilderCustom Blast
TopHatConsensus Align
BBMapRealign Region

Geneious Server runs in two configurations

Execute Host Submit Host
  • Installed on a stand-alone self-contained server.
  • Capable of scheduling jobs and performing computation.
  • Required RAM is proportional to the intensity of the analyses.
  • Connected to a cluster or other HPC facility.
  • Computation is performed externally, thereby minimizing memory requirements.

Infrastructure Requirements

  • Supports PostgreSQL, MySQL, Microsoft SQL Server and Oracle databases
  • Recommended hardware is an 8-core 64-bit Linux computer with 24Gb of RAM or higher
  • Minimum hardware is a 4-core 64-bit Linux computer with 8Gb of RAM
  • Requires Red Hat Enterprise Linux as the operating system

Benefits of Geneious Server

  • High-intensity computing tasks are handled by the server
  • Faster analysis of large volumes of sequence data
  • Your institution’s available computing power can be utilized fully
  • Server power can be shared securely amongst teams of researchers
  • Fast workflows make handling large volumes of samples easier

Geneious is an indispensable tool for organizing, analyzing and storing our diagnostics tasks and, together with the Geneious Server package, is a terrific and powerful workbench enabling efficient genomics work – a real boon for any genetics laboratory
Dr Juerg Frey, Agroscope Changins-Waedenswil Research Station – Switzerland

Case Study: Virus Hunting with Geneious Server

UCSF’s Viral Diagnostics and Discovery Center is a leader in the detection and discovery of novel viruses associated with acute and chronic human illnesses. Headed by Dr. Charles Chiu, its projects help unlock unexplained acute illnesses such as respiratory infections, gastroenteritis, and encephalitis, as well as chronic illnesses such as cancer.

“Geneious is really the perfect software package for bioinformaticians, molecular biologists, and even clinical researchers, combining both power and ease of use”

Dr. Charles Chiu, Assistant Professor, University of California, San Francisco

The lab’s origins lie in the invention of the Virochip microarray by Drs. Joseph DeRisi, PhD and Don Ganem, MD. When electron microscopy was unable to conclusively identify the SARS coronavirus, the Virochip, containing thousands of probes derived from the sequences of all known viruses, identified this novel potentially-pandemic virus within 24 hours.

In addition to using microarrays such as the Virochip, next-generation deep sequencing is a key tool for rapid, high-throughput screening. Both state health agencies and researchers worldwide regularly send samples from suspected viral outbreaks to Dr. Chiu’s laboratory for identification.

On average, the team identifies one new virus every year. One such virus was a novel adenovirus identified during a recent outbreak in Titi monkeys at UC Davis. The virus, a member of an entirely new group of adenoviruses, caused severe pneumonia among infected monkeys with a 83% case-fatality rate. Furthermore, seroprevalence studies suggested a scientist working at the center was also infected by the new adenovirus.

The Viral Diagnostics and Discovery team were also a Geneious Server private beta partner. During testing, the team used Geneious Server’s multithreaded Geneious Assembler to fully utilise the multiple processors in their 16-core, 96 GB RAM server computer. Samples analyzed by an Illumina Hi-Seq 2000 Genetic Analyzer, which generates 30 – 100 million sequence reads per sample, were aligned to known human, bacterial and viral sequences from the GenBank nucleotide database. The leftover reads were seamlessly o!oaded to the Geneious Server and assembled de novo using the Geneious Assembler. When testing their viral metagenomics workflow on a set of 17 samples from the 2009 H1N1 influenza outbreak, Geneious Assembler out-performed all of the other assemblers trialled.