Contents

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

Note that the presentations and videos may not be in sync because the presentations were updated while the videos are from previous workshops.

Introduction to Linux

  • Introduction to Linux
  • Linux file permissions

High-Performance Computing cluster

  • Introduction to HPC
  • HPC Pipelines

File types in Linux

  • File types in Bioinformatics

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 Long Reads and Pipelines

Other

  • QC of FastQ reads
  • Data management

Useful resources

  • Connecting to HPC PDC
  • Connecting to HPC UPPMAX
  • Uploading & downloading files from HPC
  • Using X11 on Windows with VcXsrv
  • Working on Tetralith: The backup cluster
  • Linux cheatsheet
  • Bash cheat sheet 1
  • Bash cheat sheet 2
  • Bash cheat sheet 3
  • Uppmax cheatsheet
  • Mac keyboard