Empowering scientists with data literacy skills in long-read genomic sequencing

Abstract

Accessibility of long-read sequencing through portable sequencers offers a significant opportunity for scientific advancement. However, the lack of data literacy among life science students presents a notable challenge. Therefore, we developed a six-week Data Literacy in Genome Research course for six cohorts, uniquely integrating wet lab and bioinformatics components, focusing on plant genomics. The course empowers students to plan, execute, and analyse a genome sequencing project using nanopore sequencing, promoting a comprehensive understanding of genomics. The curriculum begins with lectures covering genome sequencing strategies, technologies, and bioinformatics methods. Emphasising practical application, students plan their own projects. The two-week wet lab phase guides them through high molecular weight DNA extraction, quality assessments, library preparation for nanopore sequencing, and actual nanopore sequencing. The subsequent three weeks focus on bioinformatics analysis and cloud computing, encouraging the self-guided exploration of diverse tools for genome assembly, annotation, and variant detection, enabling students to choose their tools and enhancing autonomy and problem-solving skills. Emphasis is placed on learning from errors in the bioinformatics realm. Concluding in a scientific paper, peer review report, and international symposium presentation, the course highlights students’ achievements. Key educational approaches include interdisciplinary teaching, collaborative learning, research-oriented instruction, and peer feedback. Adhering to open education principles, we freely share course materials for enhanced accessibility and reuse opportunities. Continuous improvement, guided by student feedback, ensures an evolving and effective educational experience. The success is evident in students' newfound confidence in genomics and bioinformatics, emphasising the need to integrate data literacy into life science education.

Biography

Katharina Wolff is currently a doctoral candidate at the TU Braunschweig, Germany, working with Prof. Dr. Boas Pucker in the Plant Biotechnology and Bioinformatics group. Her research spans the realms of synthetic biology, plant genomics, and bioinformatics, seamlessly blending wet lab and dry lab methodologies. Within the workgroup, Katharina oversees the operations of nanopore sequencing at the facility. Her role involves leveraging her expertise in both wet lab techniques and bioinformatics to conduct thorough and comprehensive genomic analyses. Additionally, Katharina has developed and supervised a practical Data Literacy in Genome Research course in collaboration with Prof. Dr. Boas Pucker and Ronja Friedhoff.