Overview
Please be guided by the training schedule below:
Course Schedule Overview (detailed view)
S - Synchronous
A - Asynchronous
Week 1 Introduction and Fundamentals
Day 1 Resource Persons: Ken, Venice
Introduction to training (S)
Introduction to Linux (S)
Using WSL on Windows and installation guide (S)
Students install WSL and follow tutorial on Linux commandline (A)
Day 2 Resource Person: Jeff
Linux file system, hard and soft links, working directory (S)
Concept of shell, Linux processes, Environment variables, PATH variables, Shell expansion, Scripts (S)
Students practice (A)
Day 3 Resource Person: Ken
Working with text files in Linux : useful commands (S)
Practice using the doc "Practical Bioinformatics Data Skills" (A)
Day 4 Resource Person: Nikki
Using Bash to manipulate common data formats (FASTA, SAM, VCF) (S)
Day 5 Resource Person: Team
Wrap-up of basic Linux training for bioinformatics and further topics (S)
Week 2 NGS data analysis (Days 6-10)
Resource Persons: Dima, Nikki, and Ken
Introduction to Second Generation Sequencing
SNP Calling Pipeline
Filtering and basic statistics
Wrap-up
Week 3 Basic GWAS tutorial and intro to own project (Resource persons: the Team)
Week 4 Introduction to post-GWAS analysis, SNP-Seek , and continuation of project activities
Week 5 Continuation of project activitiesÂ