University of Arizona
Metagenomics: ABE 487/587
Environmental genomics is revolutionizing our understanding of microbes from the environment to human health, towards a holistic view of ecosystems or “One-Health”. At its core are new molecular methods called metagenomics to sequence DNA directly from an environmental sample, thus capturing the whole microbial community and bypassing culture. Modern (Next-Gen) sequencing technologies offer vast new datasets of short sequence reads representing these microbial communities, however many hurdles exist in interpreting data with high species complexity and specialized software for microbial metagenomic analyses. This course focuses on the science of metagenomics towards understanding (1) questions that environmental ‘omics can address, (2) approaches for metagenomic sequencing and analysis, and (3) how genes, pathways, and environmental context are translated into ecosystem-level knowledge. This course alternates between lectures on bioinformatics methods to implement a complete metagenomics project through detailed protocols, and training on a scripting language (Perl 6) for answering biological questions.