In this module, we will cover the fundamental skills needed for learning bioinformatics.
Introduction to Linux and command-line using WSL
Linux file system, hard and soft links, working directory
Concept of shell, Linux processes, Environment variables. PATH variable. Shell expansion. Scripts
Working with text files in Linux: useful commands
Using Bash to manipulate common data formats (FASTQ, SAM,VCF)
Learning contents: (all at Module 1 google drive)
Day 1 (July 4)
Introduction to Bioinformatics (slide deck)
Introduction to Linux (slide deck)
Operating System survey ( Form)
Hands-on exercise: Installing Windows Subsystem for Linux (WSL) - PDF
Hands-on exercise: Basic Linux commands, part 1 - Word document
Virtual Linux environment for commands practice ONLY : https://copy.sh/v86/?profile=buildroot
Supplemental material for virtual Linux environment
Today's recap
Day 2 (July 5)
Introduction to the Linux File System, including hands-on material (pdf)
Introduction to the Linux Shell (pdf)
Evaluation form for Day 2
Today's recap
Day 3 (July 6)
Day 4 (July 7)
Hands-on: Manipulating common bioinformatics data under Bash (pdf)
sample and assignment datasets
Reminder: 2 assignments that will be marked are required for Day 4
Today's recap
Day 5 (July 8)