We are pleased to announce the release of version 3.1.2 of MG-RAST with major changes to provide greater transparency to the underlying data and to make new features available on both the Overview and the Analysis page.

New Features

• alignment visualization now available,
• search within the metagenome analysis results for function and organism now available,
• figure and table data download is enabled in almost all places,
• new statistics available (hit coverage, alpha diversity, functional and taxonomic hits distribution).

Below we provide detailed descriptions of the new features and the changes.

Overview Page

The overview for a single dataset has been completely revamped to give a quick insight into the results of the MG-RAST analysis and make the analysis process and results more transparent. Additions include:

• Pie-chart with the sequence distribution giving the breakdown of the numbers of reads annotated as RNA and protein as well as the numbers for which no annotation was found.
  
• The analysis flowchart gives a quick graphical representation of the numbers of reads identified by different stages in the pipeline and will give you an idea of where the numbers used in the analyses tools come from.
  
• Pie-chart with the distribution of hits by functional category for COGs, KOs, NOGs, and SEED Subsystems. The numbers can be downloaded and the hierarchical representation can be viewed as an interactive graph using Krona.
  
• Pie-chart with the distribution of hits by taxonomic domains, phyla, and order for the annotations
  
• Alpha diversity is computed for each dataset summarizing the diversity of the annotations for a dataset with a single number. The data used in the computation can be downloaded.
• Text search for predicted functions or organisms within the analysis results of your metagenome

Analysis Page

Alignments

The BLAT hits on which the MG-RAST analyses are based can now be viewed on the new BLAT alignment page,

Interactive Krona display

The results of the hierarchical annotations can be displayed in a interactive pie-chart using Krona.

Bug Fixes

We have implemented a number of bug fixes, including:

• projects and collection management fixes,
• static generation of images,
• Heatmap and PCoA IDs fixed,
• QIIME download filtered based on selected database sources,
• download button for heatmap data,
• download button for PCoA values,
• barchart titles onclick action corrected,
• added private projects to metagenome select list,
• fixed sharing of jobs with multiple users with single click,
• fixed sorting of dataset IDs in PCoA.

It is over 7 months since Version 3 was released and the time has come to retire Version 2.

This will take effect on November 21st, 2011, two weeks from this announcement, after which the server will be permanently taken down. All parts of the analyses that are dynamically produced by the website will not be reproducible after this date. This includes images for the various analyses, e.g. pie-charts, heat-maps etc. as well as the data tables and some of the downloads, if you would like a copy of any of these please download them now. The data files used for the analysis will be preserved and we can make them available to the owner of the dataset for a limited time if requested.

Please email us at mg-rast at mcs.anl.gov if you have any concerns.

Thank you for using our site and we hope that you find Version 3 a worthy successor.

It is done! After months of work and countless useful interactions with many of our users, we are finally releasing our latest version of MG-RAST on Tuesday March 8.

The previous version (MG-RAST 2.0) was released in 2008 and has been used to analyze over 14,000 metagenomic data sets. Over 2000 users from more than 20 countries have submitted data.

The new release of MG-RAST builds on v2′s capabilities and adds a number of new features including

• scalable to Illumina sized data sets with 75bp and longer with robust quality control
• comprehensive support for metadata and metadata driven discovery of datasets
• unparalleled data extraction capabilities
• cloud support for back-end computing

What can you expect?

NEW DATA UPLOAD CAPABILITIES: Support for SFF, FASTQ and FASTA format data sets. The new server has been designed to handle reads of  75bp and longer, up to complete contig length. The server has been tested with individual data sets up to 50 GBp. We recommend uploading raw, unfiltered data, as MG-RAST will perform the QC steps required to clean up your data. The server also supports the use of assembled datasets.

GSC COMPLIANT METADATA: With many thousands of data sets in the system (many of them publicly available or in the process of being released), metadata is becoming more and more important in navigating the server. Version 3.0 includes support for GSC  metadata describing the sample. Users can enter metadata at time of submission or before sharing or publishing. MIMS, the minimal information about a metagenome, (or MIMARKS) is required before sharing or publishing any data sets on MG-RAST.

COMPREHENSIVE DATABASE. V3 includes such annotation resources as: SEED, KEGG, GO, INSDC, COGs, eggNOGs and IMG. Databases are updated every 3 months. Each data set is annotated with the database versions used to analyze it. Searching all these databases provides the ability to produce abundance profiles for COG categories, SEED subsystems as well as Kegg pathways based on the same computational analysis.

FEATURE PREDICTION. Identification of protein coding genes using FragGeneScan, an ab-initio gene caller (Rho, M et al., NAR, 2010, PMID: 20805240)  to identify the most likely reading frame and frame shifts for each sequence.  The similarity comparisons are then performed on the translated sequences, making the comparison both evolutionarily sensitive and computationally efficient.  Fraggenescan will identify multiple genes (called features) on lengthy fragments, permitting MG-RAST to annotate assembled contigs as well as short fragments.

CLUSTERING AND ASSEMBLY SUPPORT. V3 performs initial clustering of 90% identical protein fragments using uclust. During this operation we store the number of reads in each cluster to preserve abundances.

While version 3.0 supports the upload of assemblies (in FASTA format), we do not support performing assemblies in v3.0 (v4.0 will provide a web based assembly environment).

NEW USER INTERFACE AND TOOLS. Analyze your data and compare it to over 590 public metagenomes using a multitude of data visualization tools that allow for drilldown, data driven sub-selection of reads and data export. Users can, for example, download all reads for Lysine Biosynthesis from Actinobacteria from a specific data set.

CLOUD COMPUTING. The capability to not only speed up the analysis of current sequencing platforms, but also handle 3rd generation sequence data. Platforms are quickly moving from Gigabytes to Terabytes!!

WHAT WILL HAPPEN TO MY EXISTING  DATA: The MG-RAST team will migrate the data for the public metagenomes first, then we will migrate all private data sets. Existing sharing with other users will be retained.

THANK YOU BETA TESTERS: The MG-RAST team would like to offer our  thanks to the beta testers for providing their valuable feedback.