Users can offload sequence analysis to internal servers for dramatic speed gains.
By Allison Proffitt
February 1, 2011 | Biomatters launched their newest software package in November, Geneious Server, to analyze next-generation sequencing data, and it’s already found customers in Centers for Disease Control and Prevention (CDC) in Atlanta and Walter Reed Army Institute of Research in Maryland.
Geneious Server builds on Geneious Pro, but lets users offload large sequence analysis jobs to servers and computing clusters, harnessing institutions’ existing computational resources for dramatic speed gains.
“[Your computer] can’t handle the four terabytes of data that you would get off a sequencing machine,” Candace Toner, Biomatters’ CEO, tells Bio•IT World. “The computer just can’t physically handle that. So let’s say you want to compare 50 different genomes, but you’re not able to do that on your desktop... the Geneious Server software sits [on a server or cluster], but you’re actually connected to the server from your desktop so that you can drive it.”
Geneious can do sequence assembly, alignments, “just about anything you want it to do with next-gen sequence data that comes off the sequencing machines,” says Toner. In addition, she says that the Server brings to the table high performance modules that weren’t possible from a desktop computer. “There’s one for phylogenetics, there’s one for sequence assembly, and there’s one for next-gen sequencing.”
With the NGS module, users can perform full genome assembly using Velvet, BWA, MAQ and Bowtie, with SOAP2, SAM Tools and TopHat in development. The phylogenetics module is released with Mr Bayes and PhyML algorithms, and PAUP*, BEAST, RAxML, GARLI and SATé are coming soon. The sequence analysis module offers ClustalW, MUSCLE, MAFFT and Mauve Genome alignment with plans for SW, LastZ and Glimmer.
In January, Biomatters announced a partnership with Active Motif to support the latest version of TimeLogic’s Field Programmable Gate Array (FPGA) technology within Geneious Server. The planned DeCypher module for Geneious Server will let researchers offload large sequence comparison jobs such as BLASTX, Smith-Waterman and HMMer from their desktop to TimeLogic DeCypher cards. A single DeCypher card running on a small server can provide the performance equivalent to several hundred CPUs to accelerate discovery.
“Most of our customers utilize our DeCypher hardware and software in high-throughput annotation pipelines,” said Michael Murray, TimeLogic sales and marketing manager at Active Motif in a press release. “By partnering with Biomatters, we can provide our customers with Geneious’ additional functionality. Its user interface, upstream and downstream analysis and visualization tools for next generation sequencing data and sequence analysis in particular are of great interest to our customer base.”
Geneious Server runs on a 64-bit Red Hat Linux server and can either run as a server workstation or can submit jobs to computing clusters using the Oracle/Sun Grid Engine.
The software includes administration tools for data sharing, load prioritization, and more. Researchers have the option of running smaller jobs on their desktop or accessing the Geneious Server capabilities for larger jobs.
Geneious accepts data from all current sequencing platforms and is compatible with future sequencing technologies.
The first official Geneious Server customer is the Walter Reed Army Institute of Research in Maryland, one of the U.S. Department of Defense’s largest biomedical research facilities. Geneious Server will become an important tool in the Emerging Infectious Diseases Research Unit’s Next Generation Sequencing pipeline, which is one of the few laboratories to have deployed Roche 454 technology as 100% of its sequencing platform to sequence viral and other disease-causing pathogens.
As a genomic sequencing reference lab receiving samples from U.S. Department of Defense operations worldwide, the unit routinely sequences up to 96 barcoded viruses, achieving greater than 1.4 million long passed-key reads on each average sequencing run. Geneious Server will allow Walter Reed to efficiently manage the large data set generated from routine sequencing operation and improve the overall turnaround time to accomplish targeted sequences of worldwide origins. •
This article also appeared in the January-February 2011 issue of Bio-IT World Magazine. Subscriptions are free for qualifying individuals. Apply today.