BASIC BIOINFORMATICS COURSE
TRAINING OVERVIEW
The training general objective is to provide the basic bioinformatics skills necessary to perform bioinformatics analysis. Specifically: train the participants to use the Linux operating system, perform Linux operations and gain bioinformatics skills such as data manipulation, analysis and use of genomics-related bioinformatics software.
This is purely online internship.
COURSE REQUIREMENT
Laptop / PC
Core i3 processor or higher
4Gb memory or higher
Audio device (speaker or headphone)
Software and Internet
Web Browser
Internet speed of 5Mbps or higher
COURSE OUTLINE
Week 1 Introduction and Fundamentals
Objective: To introduce the Linux operating system and basic shell commands to equip the students in for commandline data analysis.
Introduction to Linux
Using WSL on Windows and installation guide
Linux file system, hard and soft links, working directory
Concept of shell, Linux processes, Environment variables, PATH variables, Shell expansion, Scripts
Using Bash to manipulate common data formats (FASTA, SAM, VCF)
Week 2 NGS data analysis for genotyping purposes
Introduction to Second Generation Sequencing
SNP Calling Pipeline
Filtering and basic statistics
Week 3 Basic GWAS tutorial and Introduction to Internship Special Project
Week 4 Post GWAS using Rice SNP-Seek, Rice Galaxy, and RicePilaf, and intro to own project
Week 5 Special Project
Week 6 Special Project Final Presentation