Metagenomics Workshop

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Macquarie University, NSW - 11^th - 12^th July 2017

Instructors

• Nandan Deshpande (ND) - UNSW Systems Biology Initiative, Sydney
• Paul Greenfield (PG) - CSIRO, Sydney
• Paula Moolhuijzen (PM) - Curtin University, Perth
• Katherine Champ (KC) - Bioplatforms Australia, Sydney

Timetable

Day 1 - Amplicon-based metagenomics

11^th July - Computer Lab 110, Level 1, Building E6A, Macquarie University, NSW 2109

Time	Topic	Links	Instructor
09:00	Introductions and course orientation		KC
09:15	Introduction to Metagenomics		PG
10:30	Practical: Introduction to the command line course		ND
11:00	Morning Tea
11:30	Introduction to NGS for metagenomics - overview; platforms; pros/cons		PG
12:00	Quality control: Intro to practical		ND
12:20	Practical: Quality control		ND
12:45	Lunch
13:30	Taxonomic analysis of amplicon data		PG
14:15	Practical: 16S –Cheremin tutorial: OTUs and taxonomy assignment		PM
15:30	Afternoon Tea
16:00	Practical: 16S –Cheremin tutorial: Alpha diversity and Beta diversity
17:00	Q&A and day 1 wrap-up		All

Day 2 - Shotgun Metagenomics

12^th July - Computer Lab 110, Level 1, Building E6A, Macquarie University, NSW 2109

Time	Topic	Links	Instructor
09:00	Introduction to day 2		PG
09:15	Introduction to WGS functional analysis		PG
09:45	Metagenome assembly and annotation		PG
10:30	Morning Tea
11:00	Introduction to the EBI Metagenomics portal (EMG) + Data Submission		PM
11:20	InterPro and GO for functional analysis		PM
11:30	Functional analysis using EMG- Part 1		PM
12:00	Lunch
13:00	Practical: Functional analysis using EMG - Part 2		PM
13:30	Introduction to R		ND
14:00	Practical: Mining the EMG output using R		PM
15:00	Afternoon Tea
15:30	Practical: Mining the EMG output using R (cont.)		PM
16:30	Accessing cloud computing		Craig
16:50	Q&A and workshop wrap-up		PG+All
17:00	Workshop Survey