Genomics Data Analysis

We develop and provide bioinformatics pipelines and interfaces in order to process and visualize a range of genetics, genomics and epigenomics data; these tools are operated by staff members or by end-users, who also benefit from expert assistance from the platform to analyze and interpret their data.

The panel of supported biological applications, mainly derived from high-throughput sequencing acquisition (NGS), includes:

  • Gene panel, whole-exome sequencing and whole-genome sequencing (SNPs, CNVs, rare variants);
  • RNA-seq (differential gene expression, splicing variants, long non-coding RNA, microRNA, single-cell);
  • Bisulfite-seq (methylation profile);
  • ATAC-seq (chromatin accessibility);
  • ChIP-seq (protein binding).

A few array analyses are also proposed (GWAS, transcriptomics, methylation).

Pipelines are built using a variety of tools chosen to ensure scalability, reproducibility and portability (workflow manager snakemake, package manager Conda, container manager Docker). Graphical Shiny/R applications provide users with efficient means to explore their results.

This activity is tightly linked with the sequencing data production operated by the iGenSeq core facility.