Pan African Bioinformatics Network for H3Africa

Next Generation Sequencing data analysis workshop Institut Pasteur de Tunis, March 5th-14th, 2014

General information

The H3ABioNet Train-the-trainer bioinformatics course was held on the 8th-26th July 2013 at ICIPE, Nairobi. Majdi NAGARA, a PhD student from IPT, has attended the course.

For those who were unable to attend the course in person, there was the possibility to join it via live streaming to Tunis (Institut Pasteur) and IBADAN (NABDA-Southwest Center, University of Ibadan). About 10 participants followed it at IPT.

The present course comes as a follow up of the Nairobi Course. Majdi NAGARA will - in collaboration with Mohamed ALIBI, Kais GHEDIRA, Amel GHOUILA, Yosr HAFFANI, Sonia KECHAOU and Dorra LOUATI - re-conduct the NGS analysis part (3rd week) of the initial course for participants from IPT andfor participants from the African nodes of the RIIP network (Réseau International des Instituts Pasteur).

 Objective of the Course:

The main objective of the course is to provide an introduction to Next Generation Sequencing (NGS) and addresses how to analyse and interpret the sequences data.

This course will be composed of theoretical sessions alternated by practical sessions. The course will be taught in English and will be organized in modules constituted by computer work, demonstrations and lectures. Topics include a brief introduction to the LINUX basic commands, an introduction to the use of statistical packages under R followed by an initiation to NGS technologies. The second part of this course will focus on NGS data analysis tools that are freely available. Through the hands-on practical sessions, participants will be become familiar with valuable NGS computational data analysis, including alignment, visualization and annotation tools.

 Duration: 7 working days.

 Number of participants: 20

 Course Venue: Institut Pasteur de Tunis, Tunisia

 Expenses: Coffee breaks and lunch packets will be provided.

Application: Applicants must submit a duly completed application form (see form below) send it in PDF format (saved as: YourFamilyName_FirstName_TTNGSIPT.pdf) by email to the following address:  This email address is being protected from spambots. You need JavaScript enabled to view it. .

The application form is available for download here.

 The deadline for applications is fixed to the February 20th, 2014 (5PM Tunisian time). Selected participants will be informed by e-mail.

 For further information you may contact Kais GHEDIRA ( This email address is being protected from spambots. You need JavaScript enabled to view it. ) and Amel GHOUILA ( This email address is being protected from spambots. You need JavaScript enabled to view it. ).


Workshop Program Outline

Wednesday 05/03: Linux OS (Kais Ghedira & Amel Ghouila)

  • Overview of Linux basic commands and scripts executing.

 Thursday 06/03: Basics in biostatistics (Sonia Kechaou & Dorra Louati)

  • Random variable, statistical testing, R project

 Friday 07/03: R for Next Generation Sequencing data analyses (Majdi Nagara)

  • R projects, Bioconductor packages download

 Monday 10/03: Introduction to Next Generation Sequencing (Majdi Nagara)

  • Sequence data file formats
  • Assessing sequence quality

Tuesday 11/03: Read alignment (IGV) (Majdi Nagara)

  • Sequence alignment
  • Alignment vs. assembly
  • Introduction to the Sequence Alignment Format (SAM/BAM)
  • SAM/BAM file processing
  • Visualizing BAM files
  • Assessing alignment quality

Wednesday 12/03: SAM tools (Majdi Nagara)

  • Single Nucleotide Variant (SNV) calling from alignment data
  • Annotating SNVs using databases
  • Assessing SNV quality metrics
  • SNV validation techniques
  • SNV datasets

 Thursday 13/03: Annotation and visualisation (Majdi Nagara)

  • Structural variations (Translocations) continued

  • Validation of translocations

  • Data visualization

 Friday 14/03: Other tools for NGS analysis example Galaxy (Yosr Haffani & Yosra Bouyaacoub)