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Genome-centric Metagenomics Workshop 2018
From community DNA to provisional whole genomes of microbial populations
This genome-centric metagenomics workshop will teach you how to obtain provisional whole genomes of individual populations from a mixed microbial community using metagenomics. The workshop has two sessions.
Session I : a three-day wetlab session dedicated towards wetlab work to generate metagenomic libraries. During this session, participants will have hands-on training on metagenome library preparation. Working individually, participants will create indexed shotgun metagenome libraries from genomic DNA of a mock community. They will get a behind-the-scenes look into a sequencing center and learn about library quality control, cleanup, and sample loading onto an Illumina MiSeq benchtop sequencer. The raw reads from their sequencing run will be used for Session II of the workshop. Basic wet lab skills are prerequisites for attending this session.
Session II : a five-day bioinformatics session focused on metagenomic data analysis. During this session, participants will learn to check raw sequence read quality, perform read quality control, assemble and annotate contigs, bin contigs into provisional whole genome sequences, and extract taxonomic information, functional annotations, and pathway information for each binned genomes.
Linux Boot Camp : an optional section for the participants who have registered for the bioinformaitcs session. It is designed to provide participants with the basics of linux command line interface. This will include logging into a remote server, basic file and folder operations, and executing programs and tools. The goal of the boot camp is to ensure that all participants in Session II have a basic understanding of linux and can follow the pace of other participants.
Both sessions of the workshop include seminars that provide in-depth background information and labs (wet and dry) geared towards providing hands-on experience. The bioinformatics tools used are freely available open access tools to enable participants to replicate the workflow with their own data. Interested participants can choose to register for either one or both of the sessions. This workshop is developed by The Energy Bioengineering and Geomicrobiology Group in the University of Calgary
Workshop Topic Highlights
Three-day metagenomic workshop - wetlab session (June 20 - 22, 2018):
- Shotgun metagenome library construction
- Library clean-up and size selection
- Demo of sequencing metagenome libraries on Illumina MiSeq
- Quality control and troubleshooting tips
Five-day metagenomic workshop - bioinformatics data analysis session (June 25 - 29, 2018):
- Metagenome reads quality check and quality control
- Assemble quality controlled reads into contigs
- Annotate assembled contigs
- Map quality controlled reads onto contigs
- Bin contigs into provisional genome bins
- Extract taxonomic, functional, and pathway annotations for each binned genomes
- Symposium with invited speakers (June 28, 2018)
- Time: 13:00 - 16:30
- Location: ENA103, Engineering Block A, 622 Collegiate Pl NW, Calgary, AB T2N 4V8)
Contact
Xiaoli Dong
Email: xdong@ucalgary.ca
Work phone: 1-403-2108727
University of Calgary
2500 University Dr NW
Calgary, Alberta, Canada, T2N 1N4
Where
Wet lab seeson: 5th floor in EEEL building
Bioinformatics session: Room EEEL402
750 Campus Drive NW
Calgary, Alberta
Canada