Description

This course will take students from raw DNA sequencing data through quality assurance, through to data interpretation, statistical analysis, and presentation of the results as a mock scientific article.  A background in microbiology, microbial ecology, or genetics would be beneficial.  No programming or data analysis experience is required. Students who are performing research may bring their own sequencing data to process in class.  Students will become familiar with command-line programs and basic computer programming techniques; understand bioinformatics methods such as quality trimming, assembling contigs, sequence alignment, using reference databases, and statistical comparisons; gain hands-on experience in bioinformatic analysis of DNA sequences using the R platform and its packages; primarily, DADA2, phyloseq, vegan, ggplot2; and be able to apply the knowledge gained in class to other sequence types and programs. Students may bring their own data, or some can be provided.  AVS 454 and 554 cannot both be taken for credit.

Student Learning Objectives:

After completion of the course, students will be able to:

• Use an understanding of bioinformatics methods, such as quality trimming, assembling contigs, sequence alignment, using reference databases, and statistical comparisons, to curate a data processing and analysis workflow. This may include bioinformatic analysis of DNA sequences, using the R platform and its packages, MEGA, etc. (Quantitative Literacy)
• Demonstrate proficiency in taking raw DNA sequence data through quality control steps to interpretation, and summation of the workflow and results into mock scientific journal article manuscripts. (Quantitative Literacy)
• Demonstrate scientific writing skills, specific to manuscript preparation, including incorporating instructor and peer-review comments and revisions. Submit multiple drafts and progression the ideas with each draft.
• Demonstrate skills in peer-reviewing manuscripts, including reviewing, editing, and scientific critique.

Taught annually in the fall semester

Syllabus

** Syllabus is subject to change.