The remarkable advances of Next Generation Sequencing (NGS) technologies enabled more comprehensive and profound investigation of disease and health issues at genomic level. Increased sequencing efforts have been made to better understand human pathogens and health-related virus, bacteria and other microorganisms. In recent years, new waves of intensive metagenomic sequencing projects were launched to study the whole human microbiome, such as the Human Microbiome Project (HMP). Today, researchers are facing tremendous challenges to deal with these large amounts of NGS sequence data and the derived data from massive computation.

Visualization is a powerful way to analyze large-scale research data and sometimes is the only way to describe the results. In various kinds of genomic, metagenomic, transcriptomic studies of microorganisms, mapping is a key analysis step, which is performed by aligning the sequences of a sample against a database of reference genomes. Mapping results reveal not only the identity and composition of the sample but, more importantly, also the variations between samples and references.

We have develop a novel visualization tool, MGAviewer (MetaGenomic Alignment Viewer), for analysis and comparison of mapping data, with a focus on virus and microorganisms NGS data. Compared to current visualization methods, which are often genome browsers, our method has unique advantages. This tool does not relay on a web server or a heavy relational database, which are expensive to maintain and update. This visualization tool solely uses a web browser, so it is platform-independent and requires no software installation. It analyzes mapping data from a local computer and it can be much faster than web-based genome browser for interactive use. Due to these features, this tool can be very easily applied by individual labs for their routine analysis of mapping data.

MGAviewer is currently developed by Zhengwei Zhu in Dr. Li's group (


(December 2011) MGAviewer is adopted by the CAMERA project in its FR resources.