Course Description
Course covers the use of bioinformatics to analyze microbiome data. Uses well-established bioinformatics approaches and pipelines to train graduate students, providing them with the knowledge and the tools to go from raw DNA sequencing data to ready-to-publish figures and tables. Students will acquire those skills over the course of one semester by using real-life data obtained from animal science studies.
Athena Title
Appl Microbiome Bioinformatics
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
In this course, students will use real-life DNA sequencing data obtained from microorganisms (which will be provided by the instructor), and learn how to process/analyze them, so that information can be presented and/or used in publications. The course will cover the use of well-established microbiome pipelines (e.g., QIIME 2) to perform sequence quality control, denoising, dereplication, chimera-filtering, taxonomic classification, as well as analysis of microbial evenness, richness, and diversity. Due to the applied nature of this course, students will have several computer laboratory activities. Additionally, discussions of literature involving the use of microbiome data will be carried out. The ultimate goal of this course is to train students on how to convert raw microbial DNA sequencing data into quality-filtered, cleaned data, that can be presented or shared with a non-specialized audience.
Topical Outline
I. Bioinformatics overview a. Key concepts, terminology, and applications b. Computer hardware/software specifications i. Processors ii. Random Access Memory (RAM) iii. Hard disk iv. Operating systems c. Typical hardware requirements to run bioinformatics analyses d. Microbiome bioinformatics software and pipelines II. Introduction to terminals and command lines III. Installing bioinformatics pipelines on macOS and Windows systems IV. Sequencing microbial DNA a. Different sequencing technologies (e.g., Illumina, PacBio) b. Sequencing primers c. Multiplexing (DNA barcoding) d. Single-end and paired-end sequencing V. Processing microbial DNA sequencing data a. Nucleotide quality scores b. FASTQ and FASTA files c. Generating sample metadata d. Quality-checking samples using bioinformatics tools (e.g., QIIME 2) VI. Metagenomics a. Using the 16s rRNA gene as marker (proxy for metagenomics) b. Denoising and dereplicating sequences c. Performing taxonomic analysis d. Analyzing microbial richness and diversity VII. Exporting and cleaning QIIME 2 outputs VIII. Summarizing datasets and formatting for statistical analysis IX. Acknowledging the pros and cons of microbiome studies, as well as future perspectives
Syllabus
Public CV