Microbial Community Analysis (amplicon community profiling, shotgun metagenomics/transcriptomics)

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 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 covers both the molecular laboratory techniques used to assay microbial communities (by lecture only) and their corresponding bioinformatics methodologies and analysis using command-line oriented tasks and applications.

This workshop covers microbial analysis and methodology using high throughput sequencing technologies, and ancillary topics, including:

• Differences between communty analysis with amplicons versus shotgun metagenomics and metatranscriptomics
• Experimental design
• Sequencing library preparation techniques and considerations (lecture only)
• Illumina HiSeq/MiSeq, and PacBio RS technologies=

• Hardware and software considerations
• Cloud Computing
• Review of command line operations

• Sequence data quality assurance and expectations
• Processing of amplicon reads (using the python application dbcAmplicons)
• Analysis of community structure (using R and vegan) 

• Metagenome assembly / Metatranscriptome assembly
• Metagenomic annotation / Metatranscripomic annotation (using MG-RAST)
• Post analysis and visualization (using R and matR)

Not all topics regarding microbial community analysis will be covered nor all potential software resources (Qiime will not be covered) as there are just too many. We will present a rich collection of lectures and hands-on sessions, covering both theory and tools. All analysis will be performed using the Linux command line on the Amazon Cloud (http://aws.amazon.com/). Exercises will offer the chance to explore software and protocols for high throughput microbila community data analysis.

What will I learn? … This workshop will prepare you to work independently on basic analyses, using your own computing resources or publicly available on-demand computation, such as AWS.

Who should attend? … Prior workshop participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … It is strongly recommended that participants have basic familiarity with the Linux/Unix (or Mac) command line, as well as familiarity with general biological concepts and an enthusiasm for learning about microbial data analysis!

What do I need to bring? … This workshop will be held in a computer room on the UC Davis campus, which has desktop computers running Microsoft Windows OS.  However, if you wish to bring your own laptop to use, you may do so.  We will send out specific software requirements prior to the workshop.

Can I bring my own data? … We will be providing experimental datasets for use during the workshop, this helps to keep the workshop moving. There will be time however to discuss your own datasets and how you might work with them outside of the workshop.

How  much does it cost? … The registration fee is $300 for UC and UC affiliates, $450 for other academic, government or non-profit participants and $600 for other participants. Amazon has kindly provided grants of $100 per participant for Amazon Web Services accounts. This will allow you to perform analyses during and after the course using Amazon’s resources, without purchasing your own high performance computing servers! Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Where is the workshop? … It will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated.  Attendance is limited to 36 participants in order to foster an effective learning environment and ensure sufficient one-on-one attention.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible once registration opens to ensure your place in the workshop.