AVS 590: Special Topics in DNA Sequencing Analysis Lab

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.

Course Goals and Student Learning Objectives:

  • Take raw DNA sequence data through quality control steps to interpretation, and summation of the workflow and results into mock scientific journal article manuscripts
  • Understand bioinformatics methods such as quality trimming, assembling contigs, sequence alignment, using reference databases, and statistical comparisons
  • Have hands-on experience in bioinformatic analysis of DNA sequences, including the R platform and its packages, MEGA, NCBI genome assembly, MG-RAST, etc.

Taught Spring 2020

Syllabus

** Syllabus is subject to change.

Policies

Attendance policy: Students are expected to attend lectures, but it is understood that life often precludes this.  Students may attend class virtually, through Zoom, which will be offered for each class.  Students who will miss a significant number of classes, or who require additional accommodations, may contact me to make alternate arrangements.

  • Pregnancy, lactation, and parenting: I am happy to make accommodations for students based on pregnancy, lactation, and parental needs, as well as work with the Office of Equal Opportunities. Maine state and UMaine policy allows students to breastfeed in any space, including in class. If a lactation space is required, please contact E.O. for arrangements.
  • Food insecure? Need clothes? Check out the Black Bear Exchange’s Food Pantry: https://umaine.edu/volunteer/black-bear-exchange/ or Old Town Crossroads Ministry.

Class participation: Students are expected to participate in discussions in class.  I strive to create inclusive discussions, but if students still find it challenging to participate please notify me and I will alter the discussion format as needed.

Late Assignments: Assignments will be accepted after the deadline, with a 10% reduction in grade per day.  Assignments will not be accepted after the final exam slot for this class.

Classroom policy: Supporting inclusion and community in science is an active process that involves both invitation, and support to ensure that the scientific community is and remains an equitable and inclusive place. Students are expected to conduct themselves in a professional and courteous manner, and to abide by University policies.

Campus Policies: “The University of Maine is an EEO/AA employer, and does not discriminate on the grounds of race, color, religion, sex, sexual orientation, transgender status, gender expression, national origin, citizenship status, age, disability, genetic information or veteran’s status in employment, education, and all other programs and activities.” Follow the links for more information.

Academic Honesty Statement*   

Students Accessibility Services Statement*

Course Schedule Disclaimer*

Observance of Religious Holidays/Events*

Sexual Discrimination Reporting (Long)*

Sexual Discrimination Reporting (Short)*

** I am a “mandatory reporter”.  If you disclose something to me, I am obligated to disclose to the relevant campus Title IX office.  This includes information revealed in class assignments.