Program overview

The course provides comprehensive multidisciplinary training in genome sequencing, advancing computing, programming, data reproducibility, open science, and specialized bioinformatics.

Understanding fundamental bioinformatics concepts
Develop practical skills in sequencing genome and analysis of sequencing data.
Apply bioinformatics to adress agricultural and health challenges in West Africa.
Master Linux and (bio)informatics tools for research projects.
Collaborate on practical projects to apply acquired skills.
Communicate effectively for training and knowledge transfer.
Integrate open science and reproducibility principles.

Who is this course for?

The training is open to students, biologists, researchers, and computer engineers working in either private or public sectors.
Admission Requirements:
- At least a Master’s degree or equivalent in biological sciences, human health sciences, or animal sciences.
- Bachelor’s degree plus at least 5 years of experience for professionals working in research organizations and technical ministries.”

Language

The course will be in French, but the slides and other course material will be in English.

Program structure

36 hours of distance learning
153 hours in the WAVE center

Module	Description	Hours	Instructors
Course review	General biology, Genomics basis, Genome Structure and Dynamics / Evolution, Sequencing technologies and Applications	36h
Sequencing: from library preparation to sequencing	Overview of Sequencing Technologies, RNA/DNA Extraction, Library Preparation for Illumina and ONT, Sequencing and Quality Control	30h	Martine Bangratz, Pakyendou Estel NAME, Dr. Cyrielle NDOUGONNA
Biological database	Sequence Databases (e.g., NCBI/SWISS-Prot), Blast Alignment, Primer design	12h	Dr. Ezechiel TIBIRI, Dr. Christine TRANCHANT
Introduction to Algorithmics	Introduction to algorithms, data and control structures, with simplified exercises to acquire the basics, reused later in R and Python.	8h	Dr. Ezechiel TIBIRI, Dr. Christine TRANCHANT, Dr. Koissi SAVI, Dr. Cyrielle NDOUGONNA
Linux	Basic Linux Commands, Bioinformatics Tools (e.g., BLAST), Advanced Linux (e.g., sed, awk), VCF, GFF Manipulation, slurm, Containers (Singularity, Conda)	16h	Dr. Ezechiel TIBIRI, Dr. Christine TRANCHANT, Pakyendou Estel NAME
OMICs data analysis	Diversity analysis / metagenomic analysis (ONT and illumina sequencing, Sequence Quality, Mapping, Structural Variant detection, SNP Annotation)	40h	Alexis DEREEPER, Dr Christine TRANCHANT, Dr. Ezechiel TIBIRI, Dr. Palwendé Romuald BOUA, Pakyendou Estel NAME
Data analysis and visualization in R	Read Tabular File into DataFrame, DataFrame Manipulation, Data Visualization (Plotting), R Markdown	20h	Dr. Koissi SAVI, Dr. Richard DAMIEN, Dr. Palwendé Romuald BOUA
Python programming	Variables, Display, Lists, Loops and Comparisons, Tests, Files, Modules, Functions, Containers, Dictionaries, Tuples, and Sets	20h	Julie ORJUELA, Dr. Ezechiel TIBIRI, Dr. Christine TRANCHANT, Pakyendou Estel NAME
Science reproductibility	Best Practices (Data Management, Code, Licensing), Containers (Docker, Singularity), Conda, Git, Snakemake	10h	Julie ORJUELA, Dr. Ezechiel TIBIRI, Dr. Christine TRANCHANT, Pakyendou Estel NAME, Dr. Koissi SAVI, Ndomassi TANDO

Practical sessions

A tutored project will begin in the second week with data identification and bioinformatics strategy definition, followed by workflow design, data analysis, and a final oral presentation.
Two-Month Internship: Following the 4-week course, each student will complete a supervised immersion internship supervised by two teaching tutors and a researcher from the host laboratory.

CIBiG

Program overview

Who is this course for?

Language

Program structure

Practical sessions