Dates: April 26-May 7, 2021
Topics: The workshop will cover best practices in bioinformatics analysis of amplicon-based microbial community data. Participants will learn to retrieve sequence data from the NCBI Sequence Read Archive (SRA), and will then use a BASH command-line environment on the Biomix computational cluster to perform sequence analysis. R will be used to perform downstream analysis and visualization of those data. Compositional statistical methods will be introduced and used throughout.
Format: This will be a virtual workshop that can be completed on the participant’s own time, without attending any scheduled events. Several scheduled “help sessions” (zoom) are planned throughout the two weeks – but are completely optional and will be recorded for those who cannot attend. Additional help will be available through the workshop’s Slack channels and through scheduling additional help with instructors and TA’s. This workshop will include some background lectures and theory, but is primarily intended as a hands-on bioinformatics learning experience. The amount of time required to complete the materials will vary, but is estimated to be 15-20 hours.
Prior Knowledge: No prior knowledge of microbial community analysis is required, but a background understanding of concepts in microbial ecology would be helpful. The workshop does not require prior knowledge of the BASH command line or R. However it is not meant to be a comprehensive introduction to either of these environments, and you will only receive basic background pertinent to the activities you need to perform to complete the workshop activities.
Hardware Requirements: The most computationally intensive portions of the workshop will be completed on the Biomix cluster, so most laptop/desktop computers running Windows, Mac, or Linux (no Chrome books/tablets) with at least 4GB of RAM and 2GB of free hard drive space, should be capable of completing the exercises. Some software installation will be required, so may need administrator-level access on the computer. If you have any questions regarding suitability of a computer for the workshop, please email us.
Not a good week? Or think you wouldn’t have time to complete in 2 weeks? Contact us for alternatives or to be on the waiting list for a future workshop.
Sponsored by Delaware INBRE (NIH NIGMS Grant P20 GM103446)