Equipments

Bioinformatics analysis

The Nice platform automatically provides sequencing reports tailored to specific requests, integrating differential expression analysis and quality controls:

• Sequencing quality control (FastQC, MultiQC),
• Data filtering and cleaning,
• Read alignment against a reference sequence (STAR, bowtie2, lifescope).

DNA Analysis

• Genome/Exome resequencing, alignment, detection of SNPs, indels, structural variants, CNVs, annotations.
• De novo assembly of small genomes < 50Mb (Abyss, Spades, Velvet, SOAP).

RNA Analysis

• RNA-Seq, differential expression analysis (normalization and contrasts between conditions) (STAR, Salmon, TrimGalore, Epi2me, DESeq2, limma, edgeR et IPA), functional annotation of results. Generation of an experimental report in PDF/HTML format summarizing quality controls and differential expression analysis.
• SmallRNA-Seq (miRNAs, piRNAs, snoRNAs, tRFs, ensembl ncRNAs, fRNAdb): analysis via a standardized pipeline including two-phase mapping (STAR, Bowtie2), detection and annotation of unannotated expression regions (MACS2), differential expression analysis (normalization and contrast comparison) (DESeq2, R Bioconductor package), result annotation. Provision of an experimental report in PDF format summarizing quality controls and differential expression analysis.
• de novo RNAseq (khmer normalization and trinity assembly),
• single-cell RNAseq (10x Genomics®, Parse Bioscience): normalizations, clustering, differential expression (Seurat, scanpy).

Nanopore

Analysis of data generated by Oxford Nanopore technology for the study of long reads and fine identification of isoforms. Use of dedicated tools such as Epi2Me, dorado or minimap2 as well as samtools for pre-processing, alignment, error correction and annotation. Detection and quantification of isoforms, study of transcript structure (alternative splicing, methylation), with synthesis of results. Generation of a PDF or HTML report incorporating quality controls specific to long reads (length, error rate, sequencing quality).

Spatial Transcriptomics

• In situ hybridization technologies combined with fluorescence imaging:
  • Xenium (10x Genomics®)
  • Merscope (Vizgen®)
• Normalization, clustering, differential expression analysis (Scanpy), visualization of annotated cells and transcripts within tissue (Squidpy, Xenium Explorer, Merscope Visualizer)

The results are automatically stored on the Médiante information system, which provides alignment .BAM files, coverage .BW files, xenium and merscope outputs, as well as all secondary analysis and statistical analysis files conducted in collaboration with the partner. Raw data can also be made available, and assistance is provided for submission to public databases (Gene Expression Omnibus, European Genome/Phenome Archive).

Update: July 2025