Trainings 2019 – Linux for Jedi

Linux For Jedi

This course offers to develop and enhance advanced Linux shell command line and scripting skills for the processing and analysis of NGS data. We will work on a HPC server and use linux powerful commands to allow to analyze big amount of biological data.


Basic knowledge of Linux (Linux for dummies required)


  • Connecting to a distant HPC
  • Manipuling large text files
  • Complex searching for text in a file
  • Using regular expression
  • Combining several commands
  • Writing simple shell scripts

Learning objectives

After this course, participants should be able to:

  • Work with larger data sets
  • Run existing data analysis tools using the command line
  • Using powerful text manipulation tool (sed, ask)
  • Chain and combine commands to manipulate complex data
  • Perform the same actions on many files
  • Write simple bash script

Training material


  • Christine Tranchant (CT) -
  • Gautier Sarah (GS) -
  • Ndomassi Tando (NT) -
  • Frederic Mahe (FM) -
  • Valerie Noel (VN) -


Date Location Topics Participants Instructors Links Units
2019 Montpellier, France Linux For Jedi 20 CT, GS, FM, VN, NT UMR AGAP
2018 Montpellier, France Linux For Jedi 24 GS, CT, CA, MS UMR AGAP
2018 Montpellier, France Linux For Jedi 20 CT, NT, BG, FS, GS UMR DIADE, IPME, MIVEGEC, transVIH-MI