A hands-on, integrative next-generation sequencing course: design, experiment, and analysis

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PROJECT SUMMARY/ABSTRACT The proposed six-week summer course will provide knowledge, practical skills and experience needed to train the next generation of biomedical researcher in planning, conducting and analyzing inter-disciplinary genomics experiments. Participants will be recruited nationally from advanced undergraduates, early graduate students and postdoctoral fellows from both biological and quantitative disciplines. In addition to learning genomics, statistics, informatics and programming from didactic lectures, participants will also gain invaluable experience working in small diverse groups, mentored by faculty instructors with expertise in both the biological and quantitative sciences. The workshop emphasizes recall and self-testing in gaining these skills in the hands-on computing and wet lab sessions, following pedagogical best practices of interleaved learning, spacing and low- stakes testing for learning. The workshop also emphasizes best practices in reproducible analysis, including literate programming, use of version control and automation via scripting from raw data to final report. Finally, students will be introduced to platforms for Big Data, including the use of cloud computing platforms and libraries for distributed computing such as Spark.