Metagenomics bioinformatics data analysis agenda

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Metagenomic Bioinformatics Session Agenda

Day 1 (Wednesday, August 21, 2019):

Introduction to metagenomics
Time Title Session Lead
8:30 – 9:00 Registration

  • Get name tags, course materials
  • Complete release of liability, waiver of claims, assumption of risk form
  • Complete photo consent form
  • Get wireless internet access
  • Get server account and connect to the servers

 Janine McCalder
9:00 - 9:30 Welcome and Introduction

 Dr. Marc Strous
9:30 - 10:00 Coffee Break
10:00 - 11:00 Server basics

  • Workshop computational resource overview
  • Connect to a remote server from a local pc: windows, mac, and linux
  • Set or change the PATH system variable in linux environment
  • How to run a command line program from a server and a cluster
  • File transfering between a remote server and a local pc

 Xiaoli Dong
11:00 - 12.00 Introduction to metagenomics

Dr. Marc Strous
12:00 – 13:00 Lunch
13:00 - 13:45 DNA sequencing

Dr. Joe Harrison
13:45 - 14:30 Introduction to raw sequence read processing

  • NGS data formats
  • Data quality has great impact on the downsteam analysis
  • Steps in NGS data quality control

 Xiaoli Dong
9:30 - 10:15 Hands-on exercise 1-1: Short reads quality assessment

  • Sequencing data quality assesment using fastqc
  • Go through fastqc output and explain what makes a good sequencing dataset

 Xiaoli Dong
14:30 - 14:45 Coffee Break
14:45 - 15:30 Hands-on exercise 1-2: Short reads quality control

  • Reads quality cotrol using BBTools software suite

 Xiaoli Dong
15:30 - 16:30 Work with your own data

Xiaoli Dong

Dr. Alyse Hawley

Jackie Zorz
16:30 - 17:00 Group photo

Janine McCalder
17:00 - 20:00 Networking reception with EBG and chalk talk

Food, refreshment will be served in this session. Workshop participants get to know each other and also get the oppotunities to meet all the EBG group members.


A chalk talk session will give the participants oppotunities to share their research:

  • Optional to attend
  • 5 min chalk talk followed by 3 min questions per participant

 Dr. Marc Strous


Day 2 (Thursday, August 22, 2019):

Metagenome assembly and short read mapping
Time Title Session Lead
8:30 - 8:45 Quick overview of the program for the day

 

 Jackie Zorz
8:45 – 9:30 Amplicon data analysis overview

Jackie Zorz
9:30 - 10:15 Introduction to gene-centric metagenome analysis

Dr. Alyse Hawley
10:15 - 10:30 Coffee Break
10:30 – 11:15 Metagenome sequence assembly overview

Dr. Alyse Hawley
11:15 - 12:00 Hands-on exercise 2: Assembly using Megahit

Dr. Alyse Hawley
12:00 – 13:00 Lunch
13:00 - 13:45 What makes a good assembly

How to evaluate assemblies

 Dr. Alyse Hawley
13:45 - 14:30 Hands-on exercise 3: Short reads mapping

  • Introduction to the popular short read mapping tools
  • Mapping tool input data format
  • Mapping tool output file format manipulation: sam and bam file conversion, indexing
  • Mapping tool output file visualization and coverage calculation

 Xiaoli Dong
14:30 - 14:45 Coffee Break
14:45 - 15:30 Hands-on exercise 3: Short reads mapping cont.

  • Introduction to the popular short read mapping tools
  • Mapping tool input data format
  • Mapping tool output file format manipulation: sam and bam file conversion, indexing
  • Mapping tool output file visualization and coverage calculation

 Xiaoli Dong
15:30 - 16:30 Work with your own data

Xiaoli Dong

Dr. Alyse Hawley

Jackie Zorz


Day 3 (Friday, August 23, 2019):

Metagenome binning
Time Title Session Lead
8:30 - 8:45 Quick overview of the program for the day

 

 Dr. Marc Strous
8:45 – 9:30 Metagenome binning and evaluation

Dr. Marc Strous
9:30 - 10:15 Hands-on exercise 4: Binning and evaluation (part 1): Metagenome binning using Metabat



Dr. Alyse Hawley
10:15 - 10:30 Coffee Break
10:30 - 11:15 Hands-on exercise 8: Metagenome annotation using MetaErg

  • Set up metagenome annoation jobs using MetaErg

 Xiaoli Dong
11:15 - 12:00 Work with your own data

Xiaoli Dong

Dr. Alyse Hawley

Jackie Zorz
12:00 – 13:00 Lunch
Symposium session chaired by Dr. Marc Strous. Location: EEEL 161
13:00 - 13:10 Symposium welcoming

 

 Dr. Marc Strous

University of Calgary
13:10 - 13:55 Through a glass (less) darkly: resolving wastewater nitrification through metagenomics

 

 Dr. Josh D. Neufeld

University of Waterloo
13:55 - 14:40 Defining the vaginal microbiome with genome-resolved metagenomics: Have we opened Pandora’s Box?

 

 Dr. Laura Sycuro

University of Calgary
14:40 - 15:00 Coffee Break
15:00 - 15:45 Proteomics and stable isotopes to unravel the ecology of microbial mat microbiomes

 

 Dr. Marc Strous

University of Calgary
15:45 - 16:30 Dynamics of microbiota communities during physical perturbation

 

 Dr. Carolina Tropini

University of British Columbia
6:00 - 8:30 Networking reception

Dinner will be served for workshop speakers and workshop registered participants


Day 4 (Monday, August 26, 2019):

Metgenome binning and annotation
Time Title Session Lead
8:30 - 8:45 Quick overview of the program for the day

 

 Jackie Zorz
8:45 - 9:15 Hands-on exercise 5: Binning and evaluation (part 2): Metagenome binning result evaluation using checkM

Jackie Zorz
9:15 - 10:30 Hands-on exercise 6: Binning and evaluation (part 3): Visualizing a phylogeny of binned metagenomes

Dr. Alyse Hawley
10:15 - 10:30 Coffee Break
10:30 - 11:15 Hands-on exercise 7: Binning and evaluation (part 4): how to select best bins

Dr. Alyse Hawley
11:15 - 12:00 Introduction to metagenome annotation

Dr. Marc Strous
12:00 – 13:00 Lunch
13:00 - 13:45 Introduction to MetaErg metagenome annotation pipeline

Xiaoli Dong
13:45 – 14:30 Hands-on session 9-1: Annotation result review

  • Go through MetaErg annotation result list and explain what is included in each file

 Xiaoli Dong
14:30 - 14:45 Coffee Break
14:45 – 15:30 Hands-on session 9-2: Extract individual bin annotation from the total metaerg annotation

  • How to extract annotaton results of an individual bin from the total annotation

 Xiaoli Dong
15:30 - 17:00 Work with your own data

Xiaoli Dong

Dr. Alyse Hawley

Jackie Zorz


Day 5 (Tuesday, August 27, 2019):

Metagenome annotation and data therapy
Time Title Session Lead
8:30 - 8:45 Quick overview of the program for the day

 

 Dr. Alyse Hawley
8:45 – 9:30 Metagenome annotaton interpretation

 Dr. Alyse Hawley
9:30 – 10:30 Recap/revisit/reflection of the contents covered in the workshop

 Dr. Marc Strous
10:30 - 10:45 Coffee Break
10:45 – 11:00 Workshop evaluation

Janine McCalder
11:00 – 12:00 Wrap-up: End of bioinformatics and beginning of biology

Dr. Marc Strous
12:00 – 13:00 Lunch
13:00 – 17:00 Data therapy

Work on your own data and get help from workshop organizers

 All the workshop organizers