Students from the Master BBSG II (Bioinformatique, biochimie structurale et génomique) and PhD students from AMU.


The aim of these sessions is to provide students skills to analyse large datasets on a cluster. A large part will be dedicated in the writing of reproductible workflow dedicated to sequencing data analysis.

Schedule of the course 2016-2017

Day Hour
Fri. 7 oct. 09:00 – 13:00
Fri. 7 oct. 14:00 – 18:00
Wed. 19 oct. 09:00 – 13:00
Thu. 3 nov. 09:00 – 13:00
Thu. 3 nov. 14:00 – 18:00
Thu. 10 nov. 14:00 – 18:00
Mon. 14 nov. 14:00 – 18:00


Topic Material
Introduction to Bash Ecole Bioinformatique AVIEAN: Unix
Introduction to Bash (en) Ecole Bioinformatique AVIEAN: Unix
The workflow (bash implementation, part 1) handout script1 DP script1 AG
The workflow (make implementation, part 2) GNU MAKE manual script1 DPmakefile installation
The workflow (Snakemake implementation, full) Snakemake presentation Practical


Connexion script

Additional tools

Emacs | Emacs RefCard|
Screen | screen Quick Reference|
Vi | Reference Card|
PBS/QSUB | Qsub tutorial|

Compte rendu

Les éléments pour le compte-rendu sont disponibles sur cette page. Les données sur les variants sont disponibles [ici].