Syllabus

Syllabus, learning outcomes and entry requirements

The syllabus for this workshop are as follows.

  • Working on the unix/linux command line
    • Command line navigation and related commands: cd, mkdir, rm, rmdir
    • Commonly used linux tools: cp, mv, tar, less, more, head, tail, nano, grep, top, man
    • Wildcards
    • Ownership and permissions
    • Symbolic links
    • Piping commands
  • Working on remote computing cluster
    • Logging on to UPPMAX
    • Booking resources
    • Job templates, submission and queues
    • Modules

After this workshop you should be able to:

  • Describe the basic principles of next generation sequencing.
  • Use the Linux command line interface to manage simple file processing operations, and organise directory structures.
  • Connect to and work on a remote compute cluster.
  • Apply programs in Linux for analysis of NGS data.
  • This is a national course open to PhD students, postdocs, group leaders and core facility staff.
  • A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable.