Life Technologies Partners with Ridom and Releases SeqSphere+ Software to Speed and Simplify Bacterial Typing
22 Apr 2013

Life Technologies Corporation has announced that it is partnering with Ridom GmbH (Munster, Germany) to make SeqSphere+ whole genome bacterial typing software available for Ion Torrent users. This software enables any lab to perform fast, affordable, and automated high-resolution bacterial typing on the Ion Personal Genome Machine® (PGM™) sequencer.

Up to now, typing methods have lacked discriminatory power, been difficult to standardize, or been labor intensive. SeqSphere+ automated software enables any microbiologist to use a genome-wide approach, typing hundreds to thousands of genes, resulting in higher discrimination and more accurate typing of bacteria.

"It is our aim to deliver a fully integrated turnkey solution for public health and clinical research microbiology," said Dr. Dag Harmsen, University Hospital Muenster, Germany, who is also co-managing director of Ridom and was central in sequencing the deadly E. coli O104:H4 that killed more than 40 people in Germany in 2011. "Together our solution provides an easy workflow with nearly no user intervention, delivering high-quality results using the Ion PGM System. We are excited and feel privileged to work together with the developer/vendor of the fastest evolving benchtop NGS platform, Ion Torrent."

The Ion PGM Sequencer is already in use for subtyping flu viruses by the Global Influenza Network, a collaborative effort between Life Technologies and scientists at a number of the world's leading government public health organizations, veterinary agencies and research institutes. The network focuses on increasing speed, cost effectiveness and accuracy of influenza monitoring and vaccine development. Members share tools, experience and data using the PathAmp™ FluA Reagents and the Ion PGM™ sequencer.

Bacterial typing using Ion Torrent technology is fast and affordable. Bacterial typing can be performed in less than a day from library prep to data analysis. The complete solution includes:

• Ion Xpress® Plus Fragment Library Kit for library construction
• Ion Chef® System for high throughput sequencing or Ion OneTouch® 2 System to automate template preparation
• Ion PGM® Sequencer and Ion Chips with the 400 base-pair kit for long, accurate reads in as little as three hours
• Torrent Suite Software & Ridom SeqSphere+ Software for easy data analysis & assembly.

SeqSphere+ features include:

DNA re-sequencing editor edits and analyzes de novo (.ace) or reference-mapped assemblies (.bam) of NGS data (e.g., MLST, MLST+). Auto-correction of homopolymer related InDel errors.

Analytical tools select data entries from a comparison table for epidemiologic, evolutionary or functional analysis. Cluster and visualize data entries by using minimum spanning or UPGMA/Neighbor Joining trees.

Database to store, search, retrieve, export and create reports from your epidemiologic and DNA sequence data stored in an integrated database. Search new sequence entries against stored data.

Bacteria typing is automatically performed with user defined quality parameters (e.g., coverage, stop codons, frame shift detection, etc.) using public or self-defined query libraries and task templates.

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