C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018

EVENT : C3BI Training

Main speaker: Olivier Gascuel, from C3BI, Institut Pasteur (France) Date : 22-10-2018 at 09:00 am Location: Institut Pasteur International Network – HKU Pasteur – Hong Kong

General Information:

This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have theoretical morning sessions followed by small groups practice for a few selected students with their own data. Flyer for the course: CLICK ME

Topics:

Introduction to phylogeny: General principles for the inference, interpretation of trees, and application to infectious diseases
Introduction to the math behind the trees and evolutionary models
Distance and parsimony methods
Maximum likelihood methods
Bayesian methods, phylodynamics
Branch supports, bootstrapping
How to select the best method and evolutionary model
Tree dating, reconstructing and using character evolution
Molecular epidemiology

Teachers:

Chair: Olivier Gascuel, C3BI, Institut Pasteur (France) Anna Zhukova, C3BI, Institut Pasteur (France) Frédéric Lemoine, C3BI, Institut Pasteur (France) Hein Min Tun, School of Public Health, The University of Hong Kong Julien Guglielmini, C3BI, Institut Pasteur (France) Sebastian Duchene, University of Melbourne (Australia) Tim Vaughan, ETH Zürich (Switzerland) Tommy Lam, School of Public Health, The University of Hong Kong Veronika Boskova, ETH Zürich (Switzerland)

Course dates:

Monday, October 22^nd to Saturday, October 27^th

Pre-requisites:

Basic knowledge on how to use sequence databanks
Basic knowledge using Blast and multiple alignments software
Basic knowledge of statistics (tests, distributions, parameter estimation)

Applications:

Open to postgraduate students, MD, DVM, postdoctoral fellows and young scientists from Hong Kong and overseas. The course fees are 500HK for the theory sessions and 1000HK for the full course. Students coming from the Institut Pasteur International Network will have the fees waived. Please fill in the following application form before August 20th Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018

General Information:

Topics:

Introduction to phylogeny: General principles for the inference, interpretation of trees, and application to infectious diseases
Introduction to the math behind the trees and evolutionary models
Distance and parsimony methods
Maximum likelihood methods
Bayesian methods, phylodynamics
Branch supports, bootstrapping
How to select the best method and evolutionary model
Tree dating, reconstructing and using character evolution
Molecular epidemiology

Teachers:

Course dates:

Monday, October 22^nd to Saturday, October 27^th

Pre-requisites:

Basic knowledge on how to use sequence databanks
Basic knowledge using Blast and multiple alignments software
Basic knowledge on statistics (tests, distributions, parameter estimation)

Applications:

Open to postgraduate students, MD, DVM, postdoctoral fellows and young scientists from Hong Kong and overseas. The course fees are 500HK for the theory sessions and 1000HK for the full course. Students coming from the Institut Pasteur International Network will have the fees waived. Please fill in the following application form before August 14th Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

Training – C3BI Hands-on NGS course Hong-Kong 2017

EVENT : C3BI Training

C3BI Hands-on NGS course Hong-Kong 2017

Main speaker : C3BI Training, from Institut Pasteur Date : 06/11/2017 at 09:00 am Location : Other – HKU-Pasteur Research Pole

This theoretical and practical course is aimed at researchers who would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data. Ultimately, we want this course to be of immediate value to the students. The first week of this course (Nov 6th – 10th) will be devoted to theory and practical examples for a broad audience, while the second week (Nov 13th – 17th) will be dedicated to practical analysis and hands-on for a selected group of participants. Prospective students when registering can apply for the first theoretical week only or for both weeks. Students applying for the hands-on section will be selected based on their data and the analyses they wish to perform. The course will be free for participants coming from the Institut Pasteur International Network, whereas all other students will pay 1000HKD if they assist to the first week and, 2000HKD if they take the whole course. The course will be held at the University of Hong-Kong. The official language for the theoretical and hands-on session will be English. This hands-on NGS course is open to the whole Pasteur International Network, Hong- Kong Universities and Research Centers.

Please fill the application form HERE, and send your CV and 1-2 letters of recommendation to hku-pasteur@hku.hk

Deadline for applications: September 1^st, 2017 (midnight Paris time) For more information, please contact the course secretariat at hku-pasteur@hku.hk

Course Documents

Day 1 – Introduction
- Presentation of the course – Slides
- Introduction to NGS technologies and platforms – Slides
- Introduction to Linux – Slides
Day 2 – R and statistics
- R – Slides and R code
- Basic statistics – Slides and R code
- Hypothesis testing – Slides and R code
- Experimental design – Slides
- Regression – Slides and R code
- Multiple testing – Slides and R code
Day 3 – 1st NGS day
- Library preparation – Slides
- General introduction to DNA-Seq analysis pipeline – Slides
- Quality Analysis – Slides
- Mapping and Assembly – Slides
- Analysis pipeline / intro to file formats (FASTA, SAM, BED, BAM…) – Slides
Day 4 – 2nd NGS day
- Re-sequencing and variant analysis (mapping strategies, calibration, variant calling, etc) – Slides
- Re-sequencing and variant analysis (GATK)
  - reads for variant calling
  - genome for variant calling
  - command lines for variant calling
- Gene Expression Analysis with RNA-Seq data
  - Basics in RNA-Seq – Slides
  - Differential analysis – Slides
  - Pathway analysis – Slides
- PCA and clustering with application to RNAseq – Slides – R code and data
Day 5 – 3rd NGS day
- Rare variant analysis (congenital diseases, etc) – Slides and output – Data and input:
  - Link1
  - Link2
  - Link3
- GWAS for non family based studies – Slides
- GWAS for family based designs – Slides
- Metagenomics overview – Slides