FAME Metagenomics workshop 2022

FAME Metagenomics Workshop for 2022

Welcome to the FAME metagenomics workshop for 2022, sponsored by SAGC! Follow the links in the schedule table to access the workshop material for that session. Click ‘Home’ to return here.

Download the manual



Time Topic Presenter
0900-0915 Welcome and Introductions Rob Edwards
0900-1000 Introduction to computing Bhavya Papudeshi
1000-1030 QC/QA hands-on Bhavya Papudeshi
1030-1100 Morning coffee  
1100-1130 Introduction to metagenomics (slides) Michael Doane
1130-1230 FOCUS hands-on Michael Doane
1230-1330 Lunch  
1330-1400 Functional analysis Susie Grigson/Michael Doane
1400-1430 Super-Focus hands-on Susie Grigson/Michael Doane
1430-1500 Sequence Assembly and Evaluation with QUAST (slides) Vijini Mallawaarachchi/Bhavya Papudeshi
1500-1530 Afternoon tea  
1530-1600 Metagenomic binning (slides) Vijini Mallawaarachchi
1600-1700 Binning hands-on Vijini Mallawaarachchi


Time Topic Presenter
0900-0930 Recap Everyone
0930-1000 MAG annotation using PATRIC Bhavya Papudeshi/Susie Grigson
1000-1030 KEGG mapper Bhavya Papudeshi
1030-1100 Morning coffee  
1100-1200 AMR and WW Erica Donner
1200-1230 AMR finding Michael Roach
1230-1330 Lunch  
1330-1400 Data visualization in R and Python Michael Roach
1400-1500 Hands-on data viz part 1 Michael Roach
1500-1530 Afternoon tea  
1530-1645 Hands-on data viz part 2 Michael Roach
1645-1700 Wrap up and summary Rob Edwards


Download the Snakemake Tutorial slides

Download the Snakemake Tutorial Documentation

Time Topic Presenter
0900-0930 Recap of Day 1 and 2 Rob Edwards
0930-1000 Introduction to workflows Nathan Watson-Haigh
1000-1030 Snakemake Nathan Watson-Haigh
030-1100 Morning coffee  
1100-1200 Snakemake hands on Nathan Watson-Haigh
1230-1330 Lunch  
1330-1400 SAGC Sen Wang
1400-1500 Travel to Adelaide Tree Climb  
1500-1630 Adelaide Tree Climb  
1700 Drinks at the Goodwood Park HotelSAGC