Microbial Community Analysis (Amplicon Community Profiling)

May 17, 2021, 9 a.m. - May 19, 2021, 5 p.m.

Organizer -

Bioinformatics Core

Contact -

UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

With high-throughput sequencing (HTS) of entire microbial communities we are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Using these data we are able to achieve the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms are doing) composition of microbial communities, making it possible to perform investigations that include organisms that were previously intractable with culturing-based methods.

With HTS all organisms contained in an environmental sample are sequenced in a culture-independent manner, using either amplicon based methods to investigate the taxonomic content or whole-genome/transcriptome shotgun-based methods to investigate both the taxonomic and functional content of the sampled community. This workshop will cover - the amplicon-based molecular laboratory techniques used to assay microbial communities (lecture only) - the bioinformatics methodologies for analysis using command-line tasks and applications (hands-on) Metagenomics and metatranscriptomics will be briefly covered in a lecture. Not all topics regarding microbial community analysis will be covered nor all potential software resources (Qiime or Mothur will not be covered) as there are just too many. Visit the course website for more information.

A basic understanding of the command line and R is highly recommended for success in this course. We will conduct a very brief review on the first morning of the course, but we will not be providing full instruction in basic CLI or R. To get the maximum value out of the course, intermediate knowledge of CLI and R is needed, though beginners without this prior knowledge will still achieve a thorough understanding of microbial community analysis, but may not be able to conduct an experiment on their own. For a thorough grounding in bioinformatics prerequisites, we recommend beginners enroll in our introductory courses in CLI and / or R.

The registration fee is $1,000 for current students, postdocs, staff and faculty at Univeristy of California campus' or UC National Labs (LBNL, LANL, LLNL), $1,200 for other academic or non-profit participants and $1,700 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.

This workshop will be held online from 9:00 am to 5:00 pm each day.

Registration closes on: May 14, 2021