Topics in Systematics and Evolution: Bioinformatics for Evolutionary Biology
##DESCRIPTION##
The purpose of this course is to provide graduate students with the theoretical knowledge and practical skills for the evolutionary analysis of next generation sequence data. The course will entail data retrieval and assembly, alignment techniques, variant calling, gene expression analyses, hypothesis testing, and population genomic and phylogenomic approaches. The course will be presented as a series of short lectures and lab exercises over a two week period in January.
##INSTRUCTORS##
Dr. Sariel Hubner, Dr. Sam Yeaman, Dr. Evan Staton, Dr. Loren Rieseberg
##FORMAT##
A mix of lecture and lab exercises, running in a 2-hour block.
##ENROLLMENT PROCESS##
Register for section 201 of Biol 525D.
##PREREQUISITES##
Students should have basic knowledge in R and some command line knowledge (although the latter could be obtained during the course)
##EVALUATION##
Participation in discussions and lab exercises.
##LOCATION AND TIME##
MWF (4-6:30pm) - ANGU 437 (We will not be meeting at this location due to space limitations.)
MWF (4-6:30pm) - HEBB 12
T/R (4-6:30pm) - LASR 107
##TOPICS##
Resources for each topic are in a subdirectory based on the topic.
- Broad introduction: Scope of course, goals, overview of technology and bioinformatics, and the future of sequencing [LOREN]
- Fastq files and quality checking/trimming [SAM]
- Alignment: algorithms and tools [SARIEL]
- Assembly: transcriptome and genome assembly [SARIEL]
- RNAseq + differential expression analysis [SAM]
- SNP and variant calling [SARIEL]
- Population level statistics (sliding window analyses, nucleotide diversity, FST, SFS) [SAM]
- Functional annotation and the use of ontologies [EVAN]
- Phylogenetic inference [EVAN]
- Among-species comparisons [EVAN]
- Best practices, wrap-up discussion [ALL]