Bioinformatics Tools for Shotgun Metagenomic Data Analysis

The tremendous progress in next-generation sequencing (NGS) technology has brought an avalanche of sequence-based data. This huge volume of data has resulted in novel challenges for existing bioinformatics tools in terms of data handling and subsequent analyses. Additionally, complexity of such data makes the task of analysis of metagenomic datasets more complicated for available bioinformatics pipelines. Here we are dealing with various bioinformatics tools, available online for analysis of WGS-based metagenome datasets, and simultaneously comparing their analysis pipelines. In the last one decade, over a dozen of such online tools/servers have been developed which are accessible via public domain. IMG/M and MG-RAST are two of the most popular tools as per the number of citations they received in peer-reviewed scientific journals till December 2016. This chapter discusses and compares 11 online bioinformatics tools detailing their sequence data handling, pipelines for annotation, sequence clustering methods, user-friendly attributes, and feasibility of data repository.