Genomics Data Analysis and support

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.

Our 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.

Our activity is tightly linked with the sequencing data production at the iGenSeq core facility.

Techniques

We provide support in the analysis of most high-throughput sequencing acquisition (NGS) techniques, including:

• Whole-exome sequencing and whole-genome sequencing (SNPs, CNVs, rare variants, expansions), Gene panel;
• Bulk RNA-seq (differential gene expression, splicing variants, long non-coding RNA, microRNA);
• Single-cell RNAseq, single-cell multiome (10X Genomics);
• Bisulfite-seq (methylation profile);
• ATAC-seq (chromatin accessibility);
• ChIP-seq (protein binding).
• Long-reads sequencing (Oxford Nanopore Technologies, transcriptomics)
• GWAS, transcriptomics, methylation.