A Protocol for Teaching Basic Next Generation Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R.

Next generation sequencing (NGS) is routinely used to study crucial aspects of biological systems, including differentially expressed genes identification, microbiome taxonomic composition and structure, enrichment of specific cellular functions in a given environment, and so on. Current research laboratories are facing a serious lack in the availability of properly trained researchers capable of carrying out basic NGS analysis computational pipelines. This reflects a gap in most academic curricula concerning the basics of NGS data management, analysis, and interpretation. Indeed, most of the times, the knowledge necessary to undertake these tasks is acquired through the use of one-shot tutorial, without a thorough explanation of the concepts behind the practical steps. With this protocol we aim to fill this gap by providing teachers with a hands-on protocol to guide bachelor and master students in a more focused analysis of NGS data, from basic and standard operations on sequencing reads (e.g., quality check and trimming) to more advanced analysis techniques (e.g., data normalization).