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From: The eUpdate, 3.13.2012

Genome-Sequencing Sleuth Aimed at New Pathogens

Free software has tracked foodborne illnesses around the world

It’s been used to crack the code of some of the most troublesome foodborne illness outbreaks in the world, including the rare and lethal E. coli hybrid strain that began in Germany and spread throughout Europe, Canada, and the U.S. last summer, as well as the outbreak of listeriosis traced to cantaloupes from Colorado-based Jensen Farms last autumn.

The tool is an open-source software package called the Computational Genomics Pipeline, created at the behest of the CDC by Georgia Tech associate professor of biology King Jordan, PhD, along with a team of bioinformatics graduate students.

And it’s free.

The tool is an open-source software package called the Computational Genomics Pipeline, created at the behest of the CDC by Georgia Tech associate professor of biology King Jordan, PhD, along with a team of bioinformatics graduate students.

Now used worldwide in public health research and prevention, the CG-Pipeline is an integrated software platform that allows investigators to combine the analytical power of scores of programs in a single step. It’s available online here.

“It performs work in a few days that previously could have taken months, or up to a year,” Dr. Jordan explained. The pipeline performs three steps—genome assembly, gene prediction, and functional annotation of genes—and takes multiple approaches to each of the three steps. “The depth of analysis provided by CG-Pipeline, along with its speed, are critical for effective responses to outbreaks of foodborne illnesses caused by pathogenic bacteria.”

Dr. Jordan’s team is working with the CDC to test the CG-Pipeline on a growing number of microbial pathogens; it has already been applied to cholera, Salmonella, and bacterial meningitis. The group is also trying to improve the genome assembly step to make it compatible with data produced by a variety of different technological platforms.

And, someday soon, bacterial genome sequencing may enter the “cloud.” Dr. Jordan is in discussions with Amazon about putting the CG-Pipeline on the Amazon Elastic Compute Cloud: “This would allow researchers anywhere in the world to access the power and speed of CG-Pipeline. This kind of flexibility will be particularly important in facilitating the rapid analysis of microbial pathogens that cause foodborne illness in the developing world.”

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