Life Technologies this week launched a new sequence-analysis software package for analyzing and managing data from its 5500 Series SOLiD systems, including an online portal that allows researchers to analyze their data in a cloud computing environment.
The software, dubbed LifeScope Genomic Analysis, is available under a “dual-mode use” model that allows biologists to analyze data via a graphical user interface while bioinformaticians can access more advanced features through a command-line interface.
The GUI-based option sets LifeScope apart from BioScope, Life Tech's software for previous versions of the SOLiD system, Darryl Leon, senior product manager for informatics applications, told BioInform.
While BioScope was developed for users with a programming background, Leon said that LifeScope allows users with no bioinformatics experience to set up and run workflows and view their results once the analysis is complete. The GUI and command-line modes are integrated so that bioinformaticians can create complex analysis workflows for biologist colleagues, who can then access them when they log into the software.
Life Tech plans to continue providing BioScope for customers who are using older models of its SOLiD sequencers, James Caffrey, senior manager at Life Technologies, told BioInform, although as these clients upgrade their instruments, the company will "strongly encourage" them to upgrade their software as well.
Life Tech planned to release LifeScope when it began shipping its new SOLiD sequencers in March, however the release was delayed as a result of power outages in Japan that affected its partner Hitachi High Technologies following the earthquake that struck the country earlier this year (IS 03/29/2011).
Sequences generated on the SOLiD platform are stored in XSQ (eXtensible SeQuence) format — an output file format that the company developed for the 5500 series. These files are fed into LifeScope, which then maps the individual short reads, 50 or 75 base pair fragments, to a reference genome.
The software provides tools to detect SNPs, copy number variations, small and large indels, and inversions. It also lets users perform exon counting, find junctions, detect fusion transcripts, and perform small RNA analysis as well as ChIP-seq.
Users can also track the progress of their mapping or analysis experiments and view their results in the Broad Institute’s Integrated Genomics Viewer.
One early-access user, Christian Gilissen, a researcher at the department of human genetics at Radboud University Nijmegen Medical Centre in the Netherlands, has been using LifeScope with the center's SOLiD instruments in order to study patients with hereditary diseases.
"We have a very specific focus on identifying Mendelian disease genes by exome resequencing," Gilissen said in a statement. "We have used LifeScope to fully automate the analysis of exome data, allowing our analysis to keep up with sequencing, and obtain consistent reliable results."
Users can purchase a named user license for LifeScope at $10,000 per year or a concurrent user license at $17,500 per year, which both include five user seats.
The software is available as standalone software, as a cloud-based tool, or it can be purchased preinstalled on a workstation or cluster. Life Technologies partnered with Penguin Computing to develop LifeScope's hardware options.
LifeScope Workstation is configured with a single-node, 48-core, 2.1 GHz processor with 96 gigabytes of RAM. It provides 7.5 terabytes of long-term storage, and uses 800 watts of power.
The entry-level LifeScope Cluster is a 4-node, 48-core compute cluster with 2.66 GHz Intel Xeon X5650 processors, 24 GB of RAM per node and 9.5 TB of storage. It can be scaled to 144 cores across 12 nodes, with up to 1.1 TB RAM per node and up 108 TB total memory.
The cloud offering is available under several pricing models through the portal LifeScopeCloud.com. Under a subscription model, users can pay $1,500 for 3,000 node hours per month and 3 TB of permanent disk storage. The company also offers different pay-as-you-go models, including one for $199 a month that provides access to one core of a Xeon 2.4GHz processor with 4 GB of RAM, and another that allows users to pay $0.35 per core hour.
The infrastructure for the cluster, workstation, and the cloud are all provided by Penguin Computing.
Life Tech's primary competitor in the sequencing market, Illumina, is also planning to upgrade the software for its sequencing platforms and has also signaled that it plans to migrate its analysis tools to a cloud environment.
Earlier this month, Illumina CIO Scott Kahn told BioInform that the company is developing an analysis-workflow framework for its sequencing technology that will run on both cloud and in-house infrastructures and is targeted for release later this year (BI 05/06/2011).
Life Tech plans to adapt LifeScope to work on its Ion Personal Genome Machine next.
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