Argonne National Laboratory

MG-RAST version 4.0 released

December 5, 2016

The new version of the metagenomics analysis server MG-RAST was released November 15, 2016. The release followed an open beta testing period and feedback from numerous users.

MG-RAST is an open-source automated system for processing metagenome sequence data, which then can be used for analyses ranging from phylogenetic profiling and comparisons to functional annotations and metabolic reconstructions. To date, MG-RAST has processed more than 265,000 data sets for more than 20,000 users.

Indeed, many of the new features of MG-RAST 4.0 are designed specifically to make life easier for the users. For example, instead of having to wait for the results of each parameter change, the user can now download the complete abundance profiles of selected datasets, where the data can be filtered quickly. The new myData page is equally helpful. With it, the user can view running jobs, completed studies, and news; link to a more detailed view; and quickly search for a particular dataset. And the new version of metaZen will give the user direct feedback and input help when creating metadata spreadsheets.

“We’re especially proud of the redesigned metagenome analysis page,” said Folker Meyer, a senior computational scientist in the Mathematics and Computer Science (MCS) Division at Argonne National Laboratory and founder of the MG-RAST project. He noted that all the user’s data now has provenance information, as well as multiple download options including the images and the data used to produce them. Moreover, all the technical details of the data progression through the MG-RAST pipeline are provided on the processing receipt page.

“This version of MG-RAST is built around a RESTful API and is deployed as a set of interacting containers” said Andreas Wilke, a fellow researcher in the MCS Division at Argonne. He pointed out the use of containers in the workflow component of MG-RAST that allows hitherto unknown performance and flexibility. “It is this newfound flexibility that enables a series of additional workflows that will add additional capabilities,” he said.

The new server was announced on the web at is available at