Wanted: Standards for metagenomics

Contest takes a close look at tools for metagenome analysis



Metagenomics looks at the entirety of the genomic information of a habitat. There are various methods that can be used in investigations of this type. In fact, so many of them that it is often difficult to find the best fit for a certain analysis. For this reason, scientists of the Helmholtz Centre for Infection Research (HZI) in Braunschweig, the University of Vienna and the University of Bielefeld just initiated a contest. The aim is to find the right method for an investigation more rapidly in the future.

Since classical sequencing methods work only in microorganisms that can be cultured in a pure culture in the laboratory, there is a stark contrast between the investigation of the metagenome and classical genome sequencing of selected organisms. Metagenomics takes a very new look at the genetic information of the world of microbes.

But the analysis of metagenomic data is associated with a number of issues. "There are many different methods one can use. But it is often unclear which tool is best-suited for the question on hand," says Prof Alice McHardy, head of the "Computational Biology of Infection Research" department at the HZI. She and her colleagues, Prof Thomas Rattei of the University of Vienna and Dr Alexander Sczyrba of the University of Bielefeld, therefore established an initiative titled "Critical Assessment of Metagenome Interpretation" (CAMI) that strives to use a contest to compare different computer-based methods of metagenome analysis. This is to identify the best methods and data sets for different questions and establish standards that make this kind of comparison and the selection of the proper method easier in the future.

This is important in order to simplify the analysis of the data sets in the future. "Thus far, many different data sets are used for analysis of the results of different methods. Therefore, it is often difficult to directly compare the results of different studies," says McHardy.

In the cope of the contest, the participants are to analyse identical data sets with their specific methods and then report their results.  Anybody who wishes to know how well-suited a certain method is for the analysis of the data provided is eligible to participate in the contest.  These results will be analysed by a panel of experts who will jointly define the best analytical measures for this purpose. "We want to use CAMI to make comparisons easier and to make it easier for the scientists to identify the right tool for a specific purpose in the future," say McHardy.

The contest is scheduled to commence before the end of the year; methods developers are invited to register already at www.cami-challenge.org.