Course Description
Covers the background and use of new high throughput genomic tools for environmental studies. Content and credits will vary depending on subjects covered, which are modified to meet the needs of enrolled students.
Athena Title
Environmental Genomics
Non-Traditional Format
In general, one-credit-hour modules of integrated lecture + discussion + lab will be offered. These may occur during traditional class meeting times or may be presented in a time- compressed workshop format. The number of credit hours will conform to UGA policies for lecture/discussion/lab contact hours.
Prerequisite
Permission of department
Semester Course Offered
Offered fall
Grading System
A - F (Traditional)
Course Objectives
This course is intended for graduate students at any level and from any field of study with an interest in genome technologies. Course will emphasize experimental design and use of current techniques. Course will use examples from current literature. Upon successful completion of this course, the student should be able to: • Describe design experiments using the technologies covered. • Compare, contrast and evaluate different instrumentation and approaches used to obtain the desired experimental data. • Locate and critically evaluate studies using genome technologies from the current literature.
Topical Outline
Core technologies and methods that are covered include: • Massively Parallel DNA Sequencing o Illumina (Solexa) Genome Analyzer o Ion Torrent Proton and PGM o Legacy data/techniques  Roche (454) Genome Sequencer  Applied Biosystems SOLID o New Technologies  Oxford Nanopore  Genia and Other Nanopore Platforms o De Novo Sequencing o Target Enrichment and Sequence Capture o RADseq o Amplicon Sequencing o Metagenomics o Gene Expression and Transcriptomes • Analyzing Massively Parallel DNA Sequence Data o Demultiplexing o Data Quality Trimming o 16S Microbial Community Analysis o De Novo Assemblies o SNP Calling o Software  Geneious  Galaxy Examples of additional technologies that could be covered, based on the interests of specific groups of students, include: • Microarrays and Quantitative PCR o Affymetrix o Agilent o NimbleGen o Gene Expression o Sequence Capture o Tiling Arrays • Microsatellite DNA Loci o Enrichment o Random Genome Sequencing for Marker Discovery o Primer Design o Genotyping by Capillary Electrophoresis o Analyzing the Data with GeneMapper • SNP Genotyping o Genotype by Sequencing o High Resolution Melt & other legacy methods
Syllabus
Public CV