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.