Training-Introduction to NGS data analysis

EVENT : C3BI Training – Introduction to NGS data analysis

  Time : 9:00 Р12:00 AM Starting Date : 10th of May till 28th of June

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris

The Hub of Bioinformatics, Biostatistics and Integrative Biology at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th to June 28th 2016, in the room Retrovirus No. 14, at the ground floor of Lwoff building. This course will provide a general introduction to the concepts of sequencing data analysis, alternating theory and practice on various data types: DNA-Seq, RNA-Seq, Chip-Seq, Metagenomics and HiC.

The course is aimed at people who want to get familiarized with the concepts and tools used for the analysis of sequencing data. The objective is to present the basic concepts such as file formats, mapping of sequences as well as the specific procedures for each data type. Participants are asked to come with a fully charged laptop (not enough plugs available) with the required tools already installed (ssh connection client). The list of required software will be available on the course web page ten days before the start of the session. This course is an introduction to sequencing data analysis.

Knowledge of the basic Linux command lines is highly recommended. Otherwise it is advisable to follow the introductory tutorial available here ( and on the course web page.

Required software:
  • SSH Client:
    • MacOSX: installed by default, no need to install
    • Linux: installed by default, no need to install
    • Windows: install Putty (

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Programme Course documents Evaluation



Course documents

Session 1: Next Generation Sequencing Technologies


Session 2: Mapping and Alignment

NGSTraining_Mapping File with command lines Mapping

Session 3: Chip-Seq

IntroChIPseq NGSTraining_ChIPseq File with command lines ChIP-seq

Session 4: RNA-Seq

rnaseqstat rnaseqstat rnaseqstat File with command lines for RNA-Seq mapping and counting File with R commandes for the differential analysis

Session 5: DNA-Seq

NGSTraining_Mapping File with command lines for DNA-seq analysis

Session 6: Metagenomics

C3BI Kennedy NGSTraining_Metagenomics File with command lines – 16S metagenomics and differential analysis File with command lines – Meta-assembly and comparative metagenomics

Session 7: HiC

C3BI NGS Course HiC 3C slides Practical work – HiC 3C (github)


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