Metagenomics bioinformatics data analysis agenda

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Metagenomic Bioinformatics Session Agenda

Day 1 (Monday, June 25, 2018):

Introduction to metagenomics
Time Title Session Lead
8:30 – 9:00 Registration (Room EEEL402)

  • Get name tags
  • Course material
  • Server account and access
9:00 - 10:15 Linux Boot Camp (optional to attend)

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 the workshop participants in Session II have a basic understanding of linux and can follow the pace of other participants.

 Jack Whitehead
10:15 - 10:30 Coffee Break and Registration Continue
10:30 - 11.00 Welcome and Introduction

 Dr. Marc Strous
11:00 - 12.00 Introduction to metagenomics

Dr. Marc Strous
12:00 – 13:00 Lunch
13:00 - 13.45 DNA sequencing

Dr. Paul Gordon
13:45 - 14:30 Introduction to raw sequence read processing

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

 Xiaoli Dong
14:30 - 14:45 Coffee Break
14:45 - 16:30 Hands-on exercise 1: Short reads quality assessment and quality control

  • Metagenomics raw sequence data quality assesment using fastqc
  • Metagenomics raw sequence data quality cotrol using BBTools software suite

 Xiaoli Dong


Day 2 (Tuesday, June 26, 2018):

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

 

 Dr. Srijak Bhatnagar
8:45 – 9:30 Metagenomic assembly overview

Dr. Srijak Bhatnagar
9:30 - 10:15 Hands-on exercise 2: Assembly using Megahit

Dr. Srijak Bhatnagar
10:15 - 10:30 Coffee Break
10:30 - 11:15 What is a good assembly

How to evaluate assemblies

 Dr. Srijak Bhatnagar
11:15 - 12:00 Hands-on exercise 3: Short reads mapping

  • Introduction to the popular short read mapping tools, input/ouput data format, output file visualization, and coverage calculation
  • Set up mapping, sam/bam file manipulating, and coverage calculation jobs using the quality controlled reads and the assembled contigs

 Xiaoli Dong
12:00 – 13:00 Lunch
13:00 - 13:45 Hands-on exercise 3: Short reads mapping cont.

  • Introduction to the popular short read mapping tools, input/ouput data format, output file visualization, and coverage calculation
  • Set up mapping, sam/bam file manipulating, and coverage calculation jobs using the quality controlled reads and the assembled contigs

 Xiaoli Dong
13:45 - 15:15 Workshop participant chalk talk presentations

  • Optional to attend
  • Every participant gets opportunity to present their reasearch
  • 5 min chalk talk followed by 3 min questions per participant

 Dr. Marc Strous
15:15 - 15:30 Coffee Break
15:30 - 17:00 Workshop participant chalk talk presentations cont.

  • Optional to attend
  • Every participant gets opportunity to present their reasearch
  • 5 min chalk talk followed by 3 min questions per participant

 Dr. Marc Strous


Day 3 (Wednesday, June 27, 2018):

Metgenome binning and annotation
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. Srijak Bhatnagar
10:15 - 10:30 Coffee Break
10:30 - 11:15 Hands-on exercise 5: Binning and evaluation (part 2): Metagenome binning result evaluation using checkM

Dr. Srijak Bhatnagar
11:15 - 12:00 Hands-on exercise 6: Binning and evaluation (part 3): Visualizing a phylogeny of binned metagenomes

Dr. Srijak Bhatnagar
12:00 – 13:00 Lunch
13:00 - 14:00 Hands-on exercise 7: Binning and evaluation (part 4): how to select best bins

Dr. Srijak Bhatnagar
14:00 - 14.45 Introduction to metagenome annotation

Xiaoli Dong
14:45 - 15:00 Coffee Break
15:00 - 16:15 Hands-on exercise 8: Metagenome annotation using MetaErg

  • Introduction to MetaErg metagenome annotation pipeline
  • Set up metagenome annoation jobs using MetaErg

 Xiaoli Dong
16:30 - 17:00 Lab tour



Day 4 (Thursday, June 28, 2018):

Metgenomic and beyond (special topics)
Time Title Session Lead
8:30 - 8:45 Quick overview of the program for the day

 

 Xiaoli Dong
8:45 – 9:30 Contextual data: Valuable information associated with sequence data

Dr. Emil Ruff
9:30 – 10:15 The known unknown: Uncovering viral dark matter through metagenomics

Dr. Maria Bautista
10:15 - 10:30 Coffee Break
10:30 - 11:15 Metaproteomics

Dr. Marc Strous
11:15 - 12:00 Transcriptomics/Metatranscriptomics

Dr. Paul Gordon
12:00 – 13:00 Lunch
Symposium session is chaired by Dr. Marc Strous
13:00 - 13:10 Symposium welcoming

 

 Dr. Marc Strous
13:10 - 13:55 Single-cell genomics of uncultured bacterial phyla in Canada's most extreme environments

 

 Dr. Peter Dunfield
13:55 - 14:40 Gut microeukaryotes, a missing link in microbiome studies

 

 Dr. Marie-Claire Arrieta
14:40 - 15:00 Coffee Break
15:00 - 15:45 Bioremediation capacity in municipal waste sites identified through genome-resolved metagenomics

 

 Dr. Laura Hug
15:45 - 16:30 Microbial colonization dynamics in the human gut: from metagenome-assembled genomes to cultivars and back

 

 Dr. A. Murat Eren
18:00 - 19:30 Networking reception

Dinner will be served for workshop speakers and workshop registered participants


Day 5 (Friday, June 29, 2018):

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

 

 Xiaoli Dong
8:45 – 10:15 Hands-on session 9: Annotation result review and individual bin annotation extraction

Xiaoli Dong
10:15 - 10:30 Coffee Break
10:30 – 11:30 Wrap-up: End of bioinformatics and beginning of biology

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

Participants can bring their own data for analysis and get help from workshop organizers

 Dr. Marc Strous, Xiaoli Dong, Carmen Li, Dr. Srijak Bhatnagar, Dr. Christine Sharp