Analytical solutions for Next-Generation Sequencing data

The Montreal C3G node is hosted at the McGill University and Genome Quebec Innovation Center (MUGQIC). The Montreal node is strongly involved with GenAP and has developed several genomic data analysis pipelines. Since 2011, we have completed more than 400 bioinformatics analysis projects with over 290 distinct groups of researchers across Canada. Our teams have significant experience in personalized medicine applications. These have included genome analysis and interpretation of personal genomes, technology and services to record patient presentations, RNA- and ChIP-seq data analysis, and analysis of complete human epigenomes in both germline disorders and cancers. Each year C3G co-organizes several international workshops about next-generation sequencing (NGS) data analysis.

The Montreal C3G node develops the GenAP Pipes which consist of Python scripts which create a list of jobs running Bash commands to analyze NGS data. Those scripts support dependencies between jobs and a smart restart mechanism if some jobs fail during pipeline execution. Job commands and parameters can be modified through several configuration files. We currently maintain 7 pipelines and are in the process of developing 3 others.

The Montreal C3G node also develops other bioinformatics tools:

lightbulb_outline View ideas list

Technologies

  • r
  • perl
  • awk
  • bash
  • python

Topics

  • Science and Medicine
  • bioinformatics
  • data science
  • next-generation sequencing
  • visualization
  • statistics
mail_outline Contact email

Canadian Centre for Computational Genomics 2018 Projects

  • Ruijian An
    Efficient frequency spectrum computation over large sample sizes
    The goal of the summer project is to revise the current implementation so that it can compute large frequency spectra efficiently. As a result,...
  • Arjun Karuvally
    Population genetics simulation and modeling using reinforcement learning
    The problem of population genetics can be viewed as a stochastic process. The aim of the project is to understand the reverse transition dynamics of...
  • Alan Williams
    Providing Public Accessibility for SegAnnDB
    This project will expand the public accessibility of SegAnnDB as well as work on providing integrations with the UCSC Genome Browser and Galaxy.
close

2018