Community-Analyzer

GUI based comparative metagenomics analysis platform

Overview

Community Analyzer is a GUI based Comparative Metagenomic Analysis platform that can be used to perform interactive 'on the fly' analysis of a given set of metagenomes on a PC/laptop with modest hardware configurations. The tool can not only help in grouping/clustering the metagenomes based on the taxonomic composition of their inherent microbial communities, but also in identifying microbial (or taxonomic) groups that show high positive/negative correlations in their abundance patterns (across the analyzed communities). Such insights can be used for inferring probable interaction patterns within microbial communities and for identifying the key players (or signature microbial groups) present in a given microbial community. Networks of symbiotically interacting microbes can also be identified and visualized. Moreover, users can also visualize the results of their comparative analysis using Principal Component Analysis (PCA) based graphical layouts, spring graphs, distance-based trees, bar charts, trend graphs and color coded tables. Using these functionalities, users can assess the relative contribution of each taxa in shaping the structure of the analyzed microbial communities (corresponding to each metagenomic data set), in addition to gaining insights into the probable interaction patterns between the constituent taxonomic groups. The intermediate analysis results can be easily exported as GML files, tables and images for later reference. Analysis instances can be saved as session files which can later be imported to carry out further analysis.

Download links

Windows

Linux

Video demo

Installation instructions

Community-Analyzer does not have any special requirements for its execution. The associated dependencies (databases and modules) are supplied along with the zip file containing the executables of Community-Analyzer. Note: The executables and the supplied dependencies (databases and modules) need to be in the same directory.

The tool can be downloaded as a zip file (containing the Community-Analyzer executable along with the associated programs and dependencies) from here. Community-Analyzer program is currently available for Windows and Linux operating systems.

After downloading the appropriate zip file, users need to unzip the contents. This would create a directory, called 'CommunityAnalyzer', containing the executable as well as all the dependencies needed for running the application. To run the application, users need to navigate to the extracted directory. To run the application for the first time in a LINUX based operation system, the permissions of the executable need to be changed. This can be done by right clicking on the executable, followed by selecting 'Properties' tab. Subsequently, users need to select the 'Permissions' tab, change all the access permissions to 'read and write' and select the check box that says 'Allow executing file as program'. A snapshot of the changes in the 'Permissions' dialog box is shown in the following figure. In case of a Windows operating system, users need to do simply right-click and select 'Run as Administrator'.

Citation

If you use Community-Analyzer for your work please cite the following paper :

Kuntal BK, Ghosh TS, Mande SS. Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes. Genomics. 2013 Oct;102(4):409-18. doi: 10.1016/j.ygeno.2013.08.004. Epub 2013 Aug 24. PubMed PMID: 23978768.

Disclaimer

"COMMUNITY-ANALYZER" SOFTWARE TOOL IS NOT INTENDED TO BE USED FOR TREATING OR DIAGNOSING HUMAN SUBJECTS.

"COMMUNITY-ANALYZER" or any documents available from this server ARE PROVIDED AS IS WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESS, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND FREEDOM FROM INFRINGEMENT, OR THAT "COMMUNITY-ANALYZER" or any documents available from this server WILL BE ERROR FREE.

In no event will the authors, their employers or any of the lab/office members be liable for any damages, including but not limited to direct, indirect, special or consequential damages, arising out of, resulting from, or in any way connected with the use of "COMMUNITY-ANALYZER" or documents available from this server.

The authors will try their best to maintain the privacy and confidentiality of the uploaded user data and will not use the data for any work directly or indirectly except for software debugging purpose.

Contact

For any queries/troubleshoot or bug report please direct your mails to kuntal.bhusan@tcs.com