C3G has extensive experience analyzing and organizing data from a wide range of biological assays, leveraging state of the art computation methods. We also offer a wide range of standardized and tailored analysis services to researchers, who in turn benefit from our extensive experience analyzing data from various sequencing applications. We can help you in the areas listed below

    • To get your data or public data analyzed by expert bioinformaticians
    • To plan an experiment with a sequencing provider
    • Support for collaborative grant applications.
    • Training as a service
    • Someone to develop a custom data analysis pipeline
    • To organize and distribute data

For More information:

We understand that each project is unique and no one solution fits all. For detailed information on how our Services team can help you with your project in the different areas, click on the button below.

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Since 2015, we have served many researchers, institutions and companies in different areas of bioinformatics

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Common Applications

Illustration of Heat map of differentially expressed genes.
As one of the most commonly requested services, our Services team can help you get the most out of RNA-seq data. This service typically includes:

  • Preprocessing: Alignment, assembly, quantification of expression
  • Expert QC and EDA (e.g. PCA)
  • Testing for simple or complex differential expression using linear models
  • Customized visualisations
  • Testing pathways & gene Sets
  • Other: eSNV calling, fusion detection, deconvolution, PDX, decontamination etc.
  • Others: Alternate-splicing analysis etc.

Illustration of UMAP plots colour coded by cluster ID, expression of a marker and DE gene.
(scRNA-Seq) is widely used to measure the genome-wide expression profile of individual cells. This allows us to study new biological questions in which cell-specific changes in transcriptome are important (e.g., cell type identification and heterogeneity of cell responses). Strategies for scRNA-Seq data analysis differ markedly from those for bulk RNA-Seq.

  • Our pipeline uses Cell Ranger (10X Genomics) to process 10X single-cell data and generate count matrices.
  • Our pipeline uses the R package Seurat to carry out scRNA-Seq analysis, which includes:
    • Quality-control assessment
    • Data exploration
    • Clustering and cell-type identification
    • ‘Per-cluster’ differential expression
  • Trajectory analysis is also performed to uncover continuous, dynamically changing cellular identities, using Monocle.
  • Our scRNA-Seq pipeline is also tailored to process and analyze single-cell data from different platforms.

Illustration of Microbiome profiling
Basic deliverables for amplicon-based metagenomics (16S, 18S, ITS, COI) sequencing data analysis include

  • Denoising of raw reads to ASVs using a dada2- or Qiime-based workflow
  • Taxonomy assignments
  • Functional annotations
  • Output files directly usable with Microbiomeanalyst or Calypso, allowing researchers to easily create their own tailored publication-standard figures.

We are also particularly committed to leading innovation in both metagenomics and metatranscriptomics. We offer state-of-the-art integrated analytic pipelines for amplicon-based metagenomics (16S, 18S, ITS, COI) or whole genome sequencing metagenomics (WGS), and metatranscriptomics (RNA-Seq) services.KEGG global metabolic networks (top picture) and co-occurrence networks (bottom picture) can be derived from WGS and 16S deliverables using the microbiome analyst interactive platform.

Illustration of Circos plot of an assembled and annotated genome.
We have extensive experience de novo assembling small (haploid; prokaryotes, archaea) and large (diploid; eukaryotes) novel genomes using both long read technologies and short reads for hybrid assembly approaches. 

Our toolbox also includes:

  • Detection, polishing and circularization of bacterial chromosome/s or other circular molecules (plasmid, mitochondria)
  • Refinement of de novo assembly using data from supporting technologies (ex.: Hi-C (Click here for more details)
  • Complete annotation processes (eg. PGAP for prokaryotes,  Augustus/MAKER for eukaryotes)
  • Reference-based variant detection (INDEL, SNP, large structural rearrangements, phased alleles) and multi genome comparison
  • Full-length RNA transcript isoform identification and detection of novel isoforms
  • Epigenetic base modification detection (ie. microbial/eukaryotic DNA modifications)
  • Multiplexed environmental samples (eg. species-level resolution via full-length 16S/18S rDNA, ITS regions)

Long read sequencing offered by third-generation sequencing providers (eg. PacBio (Click here for more details), Oxford nanopore (Click here for more details) allows for large and difficult to assemble regions of the genome (eg. TE’s, repeats, rRNA islands) to be captured in single long reads which can then be accurately anchored in the de novo assembly.

The addition of PacBio HiFi long reads (PacBio (Click here for more details), which are of Illumina-type quality, along with increasing progress in terms of throughput and cost reduction make long-read sequencing an attractive solution for many types of projects.

We are always eager and motivated to innovate and use the latest advancements in Sequencing technologies to allow for the greatest success with our clients and collaborators.

Illustration of Structural variant (SV) and and copy-number variant (CNV) profiles.
We have extensive experience with the identification of variants from whole genome sequencing (WGS) or whole exome sequencing (WES) data. This service generally involves:

  • Processing raw sequencing data to variant calls following the GATK  best practices
  • Detecting structural variants and CNVs
  • Annotating and filtering variants according to specific needs of the project to help with variant prioritization (e.g. de novo, compound het. in trios using the GEMINI framework.)

Publications & Examples of our work for DNA-Seq can be found in these papers: 

  • Nicolas, G., Charbonnier, C., Wallon, D. et al. SORL1 rare variants: a major risk factor for familial early-onset Alzheimer’s disease. Mol Psychiatry 21, 831–836 (2016). Click here access the paper. 
  • Monlong J, Girard SL, Meloche C, Cadieux-Dion M, Andrade DM, Lafreniere RG, et al. (2018) Global characterization of copy number variants in epilepsy patients from whole-genome sequencing. PLoS Genet 14(4): e1007285. Click here to access the paper.

Illustration of OncoPrint and circos plot showing multiple genomic alteration events in tumor samples.
By sequencing the DNA from both the tumour and healthy cells, WGS also enables the discovery of novel cancer-associated variants, including single nucleotide variants (SNVs), insertions/deletions (INDELs), structural variants (SVs), and copy number alterations (CNAs).
  • We employ a combination of callers that result in a reliable set of variants from matched tumor-normal pairs. For SNVs and INDELs calling, we applied Bcbio.variations ensemble approach with GATK MuTect2, VarDict, Strelka2 and VarScan2 calls. Variants discovered by at least two variant callers are selected.
  • Similarly, SVs are identified using multiple callers such as DELLY, LUMPY, WHAM, and SvABA were combined using MetaSV. 
  • Chromosomal and specific gene-level amplification and deletion events can be deduced from sequencing data using CNVkit, which analyzes coverage information. Our pipeline also integrates specific cancer tools to estimate tumor purity and tumor ploidy of sample pair normal-tumor.
  • The list of variants are annotated with different types of information such as genes/transcripts affected, genomic location, consequence/effect, and known variants from clinical databases (e.g., ClinVar and CIViC).
  • Our tumor-normal WGS pipeline is also applicable to patient-derived xenograft (PDX) and mouse models

For organisms lacking a good reference genome or transcriptome, we can perform de novo assembly and annotation using the latest approaches.

  • Assembly and transcript quantification with Trinity
  • Annotation using Trinotate
  • Differential expression analysis & GO/KEGG enrichment analysis
  • Customized visualisations

A few examples of publications our RNA-seq assembly services contributed to:

  • RNA-sequencing to assess the health of wild yellow perch (Perca flavescens) populations from the St. Lawrence River, Canada. [PMID: 30296762]
  • Snow crab (Chionoecetes opilio) hepatopancreas transcriptome: Identification and testing of candidate molecular biomarkers of seismic survey impact. Click here to access the publication.
  • Transcriptomic Response of Purple Willow ( Salix purpurea) to Arsenic Stress [PMID: 28702037]

Illustration of Chromatin accessibility and histone modification tracks, in control and treated samples.
Genome-wide profiles of DNA-protein interaction/histone modification and chromatin accessibility sites obtained by Chip-Seq and ATAC-Seq, respectively, provide valuable insights into the regulatory landscape of the genome.

  •   For both Chip-Seq and ATAC-Seq, we deliver a list of significant peaks that are annotated with the genomic location (distance to nearest gene and genic annotation) and motif enrichments.
  • For visualization, we generate the epigenetic tracks via UCSC Genome Browser  or WashU epigenome browser. Metagene plots and enrichment density heatmaps are also generated using ngs.plot or HOMER.
  •   Differential binding and accessibility could also be assessed by first obtaining a ‘reference peak set’ by merging peaks across samples in different groups.

These datasets can be integrated with other methods, such as RNA-Seq, for a multi-omic approach to studying gene expression.

Illustration of Chromatin accessibility and histone modification profiles within a differentially methylated region.
Epigenomics analyses also involve studying changes in DNA methylation. With our Methyl-Seq pipeline:

  •   Reads are aligned to a bisulfite-converted reference genome, and methylation levels for each CpG site are estimated using Bismark.
  •   Differential methylation is performed using simple or complex linear models

Our Methyl-Seq pipeline is also applicable to reduced representation bisulfite sequencing (RRBS) and targeted bisulfite sequencing using the SeqCap Epi system.

Illustration of Distribution of relative position in topologically associated domains (TADs).
We can help  you map long-range chromatin interactions to interrogate the genome’s 3D structure This service typically includes:

  • Preprocessing: Alignment, filtering pairs
  • ENCODE QC standards 
  • Contact maps, TAD domain annotation
  • Others: Visualization, integration with other genomics data (ChIP-Seq) ,etc.

Lalonde, Simon, et al. “Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene.” Genome biology 20.1 (2019): 1-13.

Illustration of three-dimensional structure of a protein.

We can help you with structural bioinformatics that integrates with other genomics studies. This service typically includes:

  • Structure visualization
  • Mutation mapping. 
  • MD simulation, binding energy
  • Contact maps

In addition, we also offer a wide range of services to clients as listed below

  • Other Single-Cell Assays (snATAC-seq, snDNA-seq)
  • Integrative Analyses (e.g. with SNF)
  • Expression & Methylation microarrays
  • Misc. sequencing assays: DRIPc-seq, RIP-seq, etc.
  • miRNA and other small RNA-seqs
  • CRISPR-Cas9 data  and statistical analysis 
  • Sequencing of pools (Pool-seq)
  • Population Genomics: GBS, RAD-Seq
  • CyTOF
  • Metabolomics data integration(processed data only)
  • Proteomics(same caveat as for metabolomics)
  • Rare Diseases
  • Secure Computing
  • Network Visualization and Analysis
  • Image Analysis

Our Pricing

The total cost for our services is highly dependent on the work necessary to help you reach your research goals, so please contact us to discuss the project and obtain a quote! Charges for services are calculated based on an hourly rate of $126.00 (CAD) for academic and nonprofit organizations and $147.00 (CAD) for the private sector. As a Genome Canada Technological Platform, authorship is not required, only acknowledgement.

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Partner Platforms (Wet-lab services)

McGill genome centre logo

The McGill Genome Centre provides Canadian and international researchers with high-throughput technologies and cutting-edge approaches to enable next-generation genomic studies. Initiatives led by our scientists have enabled us to secure state-of-the-art technologies and integrate innovative methodologies, shaping the future of genomics. Learn more 

Genome Quebec bilingual logo

The CES offer high-quality sequencing (including parallel sequencing), genotyping, functional genomics and nucleic acid extraction services to the scientific community. They provide complete DNA&RNA analysis services, from a few samples to several tens of thousands per week and work in close collaboration with the Canadian Center for Computational Genomics(C3G) to offer bioinformatics services. Learn more

McGill Rosalind & Morris Goodman Cancer Research Centre logo

The GCRC has developed a suite of innovation platforms featuring highly advanced technology, each managed and staffed by dedicated, highly qualified personnel. These Innovation Platforms are vital to the research conducted by our members and are also available to other researchers at McGill and to external collaborators. Please note that once you click on the link, you will be redirected to an information page about GCRC which is available only in English at this time. We apologize for any inconvenience. Learn more