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Course Syllabus
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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 one week period in August.

INSTRUCTORS

Dr. Gregory Owens, Dr. Kathryn Hodgins, Dr. Jean-Sebastien Legare

FORMAT

A mix of lecture and lab exercises, running in a 2-hour block.

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

SCRF 1328, 10am to Noon, 1pm to 3pm.

TOPICS

Resources for each topic are in a subdirectory based on the topic. Two topics will be covered per day.

  1. Topic 1 Broad introduction: Scope of course, goals, overview of technology and bioinformatics, and the future of sequencing [Greg, JS]
  2. Topic 2 Programming for biologists [JS]
  3. Topic 3 Fastq files and quality checking/trimming [Kay]
  4. Topic 4 Alignment: algorithms and tools [GREG]
  5. Topic 5 Assembly: transcriptome and genome assembly [KAY]
  6. Topic 6 RNAseq + differential expression analysis [KAY]
  7. Topic 7 SNP and variant calling [GREG]
  8. Topic 8 Population genomics and plotting in R (Part 1) [GREG]
  9. Topic 9 Population genomics and plotting in R (Part 2) [GREG]
  10. Topic 10 Phylogenetic inference [GREG]

Grading:

Consult Grading Information.

Assignments:

Consult Daily Assignments