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]