Welcome to Todos Santos!
Thank you for joining us for our computational biology and genomics workshop. Here is a summary of the topics that we are looking forward to covering over the course of the week.
Download data files for the exercises.
Monday: Introduction to high-throughput sequencing and computational biology
- 08:00-08:45 Breakfast
- 09:00-10:30 Introduction to Todos Santos and Group Discussion [Slides]
- 10:30-11:00 High-Throughput Sequencing Technologies [Slides]
- 11:00-12:00 UNIX and Command Line Tools
- 12:00-13:00 Lunch
- 13:00-16:00 Manipulating and Obtaining Genomics Data [Slides]
- 16:00-17:30 Alignment and Read Mapping
Tuesday: RNA-seq
- 08:00-08:45 Breakfast
- 09:00-12:00 RNA-seq Data Analysis I [Slides]
- 12:00-13:00 Lunch
- 13:00-17:00 RNA-seq Data Analysis II
- 17:00-18:30 Research Presentations (with Refreshments)
Wednesday: Comparative genomic analysis
- 07:00-07:45 Breakfast
- 08:00-14:00 Local Excursion to Cacti Sanctuary and El Triunfo
- 14:00-15:30 Assembly and Annotation [Slides]
- 15:30-17:00 Variant Calling [Slides]
Thursday: Comparative genomic analysis (cont.) and Data Visualization
- 08:00-08:45 Breakfast
- 09:00-10:30 Local BLAST and Comparative Genomics [Slides]
- 10:30-11:00 Discussion on Experimental Design
- 11:00-12:00 Metagenomics and Microbial Diversity [Slides]
- 12:00-13:00 Lunch
- 13:00-14:30 Introduction to R, R Markdown, and Data Visualization [Slides]
- 14:30-15:15 Plotting Genomic Data with R and ggplot
- 15:15-16:00 Figure Drawing in R
- 16:00-17:00 Circular Representations of Genomic Data with Circos
- 17:00-20:00 Workshop Dinner
Friday: Scripting and GitHub
- 08:00-08:45 Breakfast
- 09:00-10:00 Code Management (GitHub)
- 10:00-12:00 Bash Scripting [Slides]
- 12:00-13:00 Lunch
- 13:00-17:00 Python Scripting [Slides]
Supported by the Society of Molecular Biology and Evolution, Colorado State University, and the National Science Foundation