Contents

Course materials organised by topic. When following a live workshop, use Schedule.
Slides: / , Labs: , Videos:

Introduction to Linux

  • Introduction to Linux

File types in Linux

  • File types in Bioinformatics
  • Linux file permissions

Uppmax

  • Introduction to UPPMAX
  • UPPMAX Pipelines

Advanced Linux

  • Better terminal experience
  • Advanced Linux

Variant-calling workflow

  • Variant-calling

RNA-Seq workflow

  • RNA-Seq workflow
  • Simon’s report

NGS technologies

  • NGS technologies and challenges
  • NGS Pipelines

Other

  • QC of FastQ reads
  • Data management

Useful resources

  • Connecting to Uppmax
  • Uploading & downloading files from Uppmax
  • Working on Tetralith: The backup cluster
  • Linux cheatsheet
  • Bash cheat sheet 1
  • Bash cheat sheet 2
  • Bash cheat sheet 3
  • Uppmax cheatsheet
  • Mac keyboard