"The Metagenomics Days": a simplified workshop on amplicon sequencing analysis with open cloud bioinformatics for eDNA and Microbiomes

Abstract

The "Metagenomics Days" event was organized to enhance understanding of metagenomics and microbiome analysis among participants new to the field. This paper presents an evaluation of the courses impact through a comprehensive survey administered before and after the event. We assessed participants prior knowledge, experience with bioinformatics tools, and confidence levels regarding key concepts in microbiome analysis. Word clouds generated from open-ended survey responses provided additional insights into participants interests and pre-course familiarity with metagenomic tools and concepts. Surveys results showed substantial improvements in participants confidence, particularly in building bioinformatics pipelines (+41%), understanding diversity metrics (+44.1%), and applying microbiome analysis concepts (+34.8%). Similarly, understanding of core topics like cloud computing (+28%), bioinformatics workflows (+34%), and 16S rRNA gene variable regions (+27.5%) increased significantly. The courses impact on knowledge retention was also evaluated, with participants achieving an average of 64.87% correct responses, with 25.76% unsure answers and only 9.35% incorrect responses, highlighting the effectiveness of the course in enhancing comprehension. Overall, the survey results indicate a significant increase in participants confidence and knowledge acquisition, particularly in the areas of cloud computing, diversity metrics, and bioinformatics pipelines. These improvements in confidence and knowledge acquisition underscore the effectiveness of the course in bridging knowledge gaps and preparing participants for future research in the complex and rapidly evolving fields of metagenomics and microbiome analysis.