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We analyse genetics, genomics and epigenomics data, and build the bioinformatics pipelines and interfaces that process and visualize it. Our pipelines use snakemake, Conda and Docker so that analyses stay scalable, reproducible and portable, and Shiny/R applications let you explore your own results. We work closely with the sequencing data production at the iGenSeq core facility.
Talk to us before you generate data
If you are using a technology for the first time, consult us at the design stage. We will help you choose the technology that fits your research question and ensure parameters and experimental design that will allow the analysis. Getting this wrong is expensive: sequencing that is underpowered, wrongly designed, or unsuited to the question cannot be repaired with analysis. Early contact also lets us schedule your project, so that someone is available to work on the data when it arrives.
Service catalogue
The table below lists our standard analyses and the processing steps each one covers. Services in the first group are quoted per sample, since the pipeline is standardised and the work scales with the number of samples. The price covers more than the configuration, and running your data: it also covers the development and maintenance of each pipeline, and keeping it current with new and updated features, so that what you get back is reproducible, validated and state-of-the-art. Services in the second group are quoted per hour, as is any custom or advanced analysis, development specific to your project, figure preparation, or consulting.
| Service | Processing included |
|---|---|
| Quoted per sample | |
| mRNA | Quality control, alignment, quantification, Quby |
| miRNA | Quality control, alignment, quantification, Quby |
| lncRNA | Quality control, alignment, transcript catalog generation, quantification, Quby |
| Cellranger | Quality control, alignment, quantification and report, summary sample reports |
| Cellranger preseg | Cell counts per sample |
| scRNA core | Clustering, marker identification, Quby |
| CITEseq | Cell quality control, filtering, CITE integration, clustering, marker identification, Quby |
| WES | Quality control, alignment, germline variant calling (DRAGEN), annotations (VCF) |
| WGS | Quality control, alignment, germline variant calling (DRAGEN), annotations (VCF) |
| ATACseq | Quality control, alignment, peak calling, peak annotation, differential accessibility analysis |
| Quoted per hour | |
| WGS Pacbio | Quality control, alignment, germline variant calling (DRAGEN), annotations (VCF) |
| Methylation | Quality control, alignment, differential methylation analysis |
| Spatial transcriptomics | Quality control, basic segmentation, alignment, clustering, annotation, differential expression |
| All technologies | Custom or advanced analysis on any of the above, and on gene panel, ChIP-seq, long-read sequencing (Oxford Nanopore) and GWAS |
Request a quote
We do not publish fixed prices, because a quote depends on what your project actually needs: whether the per-sample rate applies as it stands, and how much additional time is expected. Send us your project details using the request form to request a quote.
QUBY
QUBY lets you explore RNAseq, single-cell and WES data analysed by DAC yourself, without writing code. Access to QUBY is included in the mRNA, miRNA, lncRNA, scRNA core and CITEseq services.
DEJAVU
DEJAVU aggregates short variants from exome and genome sequencing across 3000 samples from ICM projects. Available to ICM researchers only.
GEO submissions
We assist researchers in uploading their data to GEO to share their data with their publications. We do so once per month. To ensure timely registration please request so at least one month in advance. Last minute requests (< 30 days) are subject to billing. Please find instructions for GEO submission here.
Contact information
Please use this form to request analysis services. For further questions, please contact us at dac_omics@icm-institute.org.