Along with its data analysis services, the Canadian Centre for Computational Genomics (C3G)  has developed and contributed to various user-oriented tools and software solutions for the genomics community. We also maintain an up-to-date set of bioinformatic tools and genomic resources. These resources are available through our partnership with Compute Canada in all their HPC clusters. Below is a comprehensive list of tools we have developed.

GenPipes logo

GenPipes was developed as a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High-Performance Computing clusters and the cloud. GenPipes comes with 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, WGS, WES, ChIP-Seq, and HiC.

Please note that the supporting documentation provided below are available in English language only.

> GenPipes: Getting Started Guide

> How to deploy GenPipes

> GenPipes User Guide

> GenPipes Tutorials

GenPipes in the Cloud logo

To facilitate deployment of our GenPipes pipelines in different computing environments, we have released GenPipes in the Cloud using Google Cloud Platform infrastructure.

Please note that the technical documents listed below are available in English language only.

> Deployment Options

> Deploying GenPipes in the cloud

> Accessing GenPipes on Compute Canada Servers

> Deploying GenPipes locally in your server

> Deploying GenPipes in a container

CVMFS logo

The Canadian Centre for Computational Genomics (C3G)  in partnership with Compute Canada, offers and maintains a large set of bioinformatics resources for the community. This includes many popular bioinformatics tools and reference genomes, including legacy versions as well as current releases. Using CVMFS, users can use this software without having to worry about installation.

Please note that the technical documentation listed below for both CVMFS Modules and Genomes are available in English language only.

 > CVMFS Modules

 > CVMFS Genomes

Bacterial Genome Synchronizer logo

The Bacterial Genome Synchronizer allows you to provide your bacterial genome and a desired start sequence, and realign the genome to start at this sequence. It also reverses your genome if it appears to be in the opposite direction to your start sequence.

Please note that this tool is accessible in English language only.

 > Bacterial Genome Synchronizer

The bacterial-genome-reconstruction tool is a web application that allows you to identify which bacterial genome has been sequenced through the BLAST tool. It also allows you to optimize the read length of your sequences to identify which length offers the greatest match percentage.

Please note that this tool is accessible in English language only.

> Bacterial-genome-reconstruction

Bento is a collection of free and open source microservices used to construct data-focused platforms. By adhering to existing and anticipated standardized APIs, it facilitates interactions between various-omic science global communities. Its reusable and interoperable components reduce the complexity and overhead of constructing data distribution portals.

Please note that this tool is accessible in English language only.

>Bento

Phenome Central logo

PhenomeCentral is a repository for clinicians and scientists working in the rare disorder community. PhenomeCentral encourages global scientific collaboration while respecting the privacy of patients profiled in this centralized database.

Please note that detailed information regarding this tool is available in English language only.

 > PhenomeCentral

PhenoTips logo

PhenoTips is a software tool providing an easy-to-use Web interface and standardized database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions.

> Phenotips

PopSV logo

PopSV is a Copy-Number Variation (CNV) detection method from high-throughput sequencing. Abnormal Read-Depth signal is detected by using a population of samples as reference.

Please note that the listed technical documentation is available in English language only.

> PopSV

Seq2Fun logo

Seq2Fun is an ultra-fast functional profiling tool for RNA-Seq data analysis for non-model organisms. The focus is on providing actionable results, without having to assemble a transcriptome de-novo.

Please note that detailed information regarding this tool is listed in English language only.

> Seq2Fun

BVA tools logo

BAM and Variant Analysis Tools kit provides a list of useful functions designated to facilitate the analysis and interpretation of next-generation sequencing data.

Please note that the technical documentation for this tool is available in English language only.

> BVA Tools

PeakSeg logo

PeakSeg is a constrained maximum Poisson likelihood segmentation model for analyzing ChIP-seq data.

Please note that the associated technical documentation is available in English language only.

> PeakSeg

PeakSeg Joint logo

Supervised segmentation for jointly finding peaks in several ChIP-seq samples.

Please note that the associated technical documentation is available in English language only.

> PeakSeg Joint

SCoNEs logo

SCoNEs is a R tool dedicated to estimate the Copy Number Variation in whole genome sequencing paired cancer data using a read depth approach.

Please note that the associated technical documentation is available in English language only.

> SCoNES

SilVA logo

SilVA is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA bases its predictions on a number of features, including CpG, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy.

Please note that the associated technical documentation is available in English language only.

> SilVA

CReSENT logo

Developed with Dr Trevor Pugh’s team at the University Health Network (UHN), CReSCENT is a web-based toolkit for analysis and visualization of single-cell expression in cancer. It uses public datasets and preconfigured pipelines that are accessible to computational biology non-experts. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.

Please note that the associated access is available in English language only.

> CReSCENT

EpigenCentral logo

EpigenCentral is a web portal that uses machine learning and predictive models to analyse epigenetic data and detect patterns related to diseases. It is built in collaboration with Rosanna Weksberg lab and is intended as a knowledge base of epigenetic signatures in neurodevelopmental disorders for the broad biomedical community and clinical practitioners.

Please note that the associated technical documentation and access is available in English language only.

> EpigenCentral

STAGER is a web dashboard developed for the sharing, monitoring and analysis of genomic and exomic datasets that are part of the Care4Rare project. Users can upload datasets and request various analyses of the data via automated pipelines.

Please note that the associated technical documentation and access is available in English language only.

> Stager

Data Privacy Assessment Tool for Health (D-PATH) is an online tool to help researchers who collect, store, own, manage or use health data, get started in the process of meeting the applicable ethical, legal, professional requirements associated with the protection of those data’s privacy and, with this, enable responsible data sharing practices.

Please note that the associated technical documentation and access is available in English language only.

> D-PATH