Sifting Through Metagenomes using the iPlant Discovery Environment

Teaching undergraduate and graduate students about metagenomics and analyzing sequence data can be challenging when participants are not familiar with the software. The iPlant Discovery Environment provides a user-friendly yet powerful platform to begin to perform metagenomic analyses in a classroom setting. Since the fall of 2013, the 8-week metagenomics course at the North Carolina State University Biotechnology Program has used the iPlant Discovery Environment to introduce students to cloud-based computing. A series of computer activities based on worksheets familiarize students with procedures to download sequences from databases, assess the quality of next-generation sequencing reads, launch applications to analyze sequences to infer taxonomy, and assemble metagenomes. Students learn key procedures in an environment that is user-friendly. Sharing of large sequence files and results with groups of students allows instructors to easily manage laboratory sessions. Pairs of students are then tasked with diagramming the procedures they followed to reinforce the steps for each workflow and propose alternatives. Combined with reflective questioning, diagramming helps students break down complex processes into simple steps. The iPlant Discovery Environment offers an increasing number of tools for analyses of next-generation sequencing data, genomics, and metagenomics on a platform that is user-friendly, powerful, and promotes interaction among student groups.