Informatics on High-Throughput Sequencing Data

Welcome

Welcome to Informatics for High-throughput Sequencing Data 2019 workshop.

The course schedule can be found here.

Meet your faculty here

CLASS MATERIALS: You can download and print the course manual here.

Pre-Workshop Materials

Laptop Setup Instructions

Instructions to setup your laptop can be found here.

Pre-workshop Tutorials

Pre-readings and pre-work can be found here here.
It is in your best interest to complete these before the workshop.

Class Photo

Day 1

Welcome

Michelle Brazas

WiFi

1) Eduroam account; or
2) Sign up for a McGill 24hr account at : https://www.mcgill.ca/it/get-help/forms/guest-wifi

Module 1: Introduction to High-throughput Sequencing

Jared Simpson

Lecture

Module 2: Data Visualization

Rob Syme

Lecture

Lab Practical

Lab Answer Key

Places to Eat

Pizza Bros https://www.pizzeriabros.ca (1212 Avenue Union)
Falafel avenue http://falafelavenue.com/en/ (2020, rue Robert-Bourassa (at University)
Japote: http://www.japote.ca (1000 Rue Sherbrooke Ouest)
Opanio: https://www.opianomtl.com (1115 Sherbrooke St W)
KoaLua: http://www.koalua.ca (1212 Avenue Union)

Module 3: Genome Alignment

Guillaume Bourque

Lecture

Lab Practical: Connecting to the Cloud

Lecture - AWS

We have set up instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. The certificates will be uploaded to Slack. If you plan on using Linux or Mac OS X, Please use CBWHT.pem; Otherwise if you plan on using Windows (with Putty), please use CBWHT.ppk.

You can also download from here. Mac/Linux certificate, Windows certificate.

Lab Practical

Integrated Assignment

Day 2

Module 4: Small-Variant Calling and Annotation

Guillaume Bourque

Lecture

Lab Practical

Module 5: Structural Variant Calling

Guillaume Bourque

Lecture

Lab Practical

Module 6: De Novo Assembly

Jared Simpson

Lecture

Lab Practical

Supplemental

Post Workshop

Post workshop content for data sets, docker containers, AWS image, tools and install instructions can be found here

Thank you for attending the Informatics on High-Throughput Sequencing Data workshop! Help us make this workshop better by filling out our survey.