Welcome to Todos Santos!
Thank you for joining us for the 2018 Computational Biology and Genomics Workshop. Here is a summary of the topics that we are looking forward to covering this week.
Download data files for exercises here.
Monday: Introduction to high-throughput sequencing and computational biology
- 09:00-10:30 Introduction to Todos Santos and Group Discussion [Slides]
- 10:30-11:00 High-Throughput Sequencing Technologies [Slides] [Genomics and NGS Glossary]
- 11:00-12:00 UNIX and Command Line Tools [Unix Resources]
- 12:00-13:00 Lunch
- 13:00-16:00 Manipulating and Obtaining Genomics Data [Slides]
- 16:00-17:00 Experimental Design for Genomics Research [Slides]
Tuesday: Comparative (meta)genomic analysis
- 09:00-10:30 Alignment and Read Mapping
- 10:30-12:00 Assembly and Annotation [Slides]
- 12:00-13:00 Lunch
- 13:00-15:00 Variant Calling [Slides]
- 15:00-17:00 Local BLAST and Comparative Genomics [Slides]
Wednesday: Microbiome analysis
- 09:00-13:00 Local excursion to Cacti Sanctuary and El Triunfo
- 13:00-14:00 Lunch
- 14:00-14:30 Metagenomics Overview [Slides]
- 14:30-17:00 16S rRNA Amplicon Sequencing and Microbial Diversity
Thursday: Data visualization and RNA-seq
- 09:00-09:30 Introduction to R, R Markdown, and Data Visualization [Slides]
- 09:30-10:15 Plotting Genomic Data with R and ggplot
- 10:15-11:00 Figure Drawing in R
- 11:00-12:00 Circular Representations of Genomic Data with Circos
- 12:00-13:00 Lunch
- 13:00-17:00 RNA-seq data analysis [Slides]
Friday: RNA-seq (cont.), Scripting and GitHub
- 09:00-12:00 RNA-seq data analysis (cont.)
- 12:00-13:00 Lunch
- 13:00-14:00 Bash Scripting [Slides]
- 14:00-15:30 Python Scripting
- 15:30-16:00 Code Management (GitHub)
- 16:00-18:00 Informal Project Discussions
Supported by the National Science Foundation (MCB-1733227).