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Advanced Linux and Bash Initiation#

Course overview#

GitHub repository 15 - 16 May, 2023

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.

Program#

  • 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

Application#

This is an SouthGreen course. The course is open for PhD students, postdocs, group leaders and core facility staff related to the SouthGreen Platform (IRD, CIRAD, INRAE and the Alliance Bioversity international-CIAT).

If we receive more applications than we can accommodate, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course. We also take in consideration a balance between the different institute and department.

Please note that SouthGreen training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Prerequisites:#

Basic knowledge of Linux (Linux for dummies required)

By accepting to participate in the course, you agree to follow the Code of Conduct.

Schedule#

You can find the course schedule at this page.

Location#

This course round is given on site. More information can be found at this page.

Course material#

The pre-course setup page lists all the information you need before the course starts. The most important part is the installation and setup of all the tools used in the course, so make sure you've gone through it all for the course start.

Teachers#

  • Bruno Granouillac (course leader)
  • Guilhem Sempere
  • Jacques Dainat

Contact#

To contact us, please send a mail using the contact form available here.