Standard Operating Procedures for Effective Galaxy Workflows

Next-generation sequencing (NGS), a widely used and cost-effective technology, has opened a window into the role of molecular genetics in understanding contrasting cellular conditions. The widespread adoption of this technology has led to a surge in biological big data, necessitating computational tools to extract meaningful patterns and relationships. Despite the availability of numerous computational tools, data analysis demands advanced programming skills and computational power, creating a divide between experimental and computational biologists. Bridging this gap is Galaxy, an open web-based platform hosting a plethora of established tools that assist in NGS data analysis in a user-friendly manner. Known for providing a comprehensive framework for batch operations on datasets through reproducible and shareable workflows, Galaxy's popularity is further bolstered by the community-driven ToolShed. This chapter focuses on the Galaxy platform's utility in deciphering the complexity of sequencing datasets, the applicability of existing NGS workflows, and the opportunities for training and teaching using preset workflows. It also highlights the platform's adaptability to the evolving landscapes in bioinformatics tool design and its prospects within the global Galaxy community.