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Cancer Genome Analysis Informatics Guide

Software used during the course

Software Version (if not latest) Module Notes
R 4.3.3 Statistical Computing Required for many bioinformatics tools
RStudio 4.3.3 IDE for R Recommended for R users
Samtools 1.9 NGS Analysis Used for BAM file processing
BCFtools 1.9 Variant Calling Works with VCF/BCF files
GATK 4.6.1.0 Variant Calling Genome Analysis Toolkit
dndscv Latest Mutation Analysis dN/dS ratio calculations
CIBERSORT Latest Deconvolution Immune cell type estimation
maftools Latest Mutation Analysis Visualization of somatic mutations
VEP (Variant Effect Predictor) Latest Variant Annotation Provided by Ensembl
SnpEff 5.2 Variant Annotation Predicts variant effects
BWA 7.18 NGS Alignment Aligns sequences to reference genome
SigProfilerExtractor Latest Mutation Signatures Extracts mutational signatures
SigProfilerMatrixGenerator Latest Mutation Signatures Generates matrices for signature analysis
SigProfilerAssignment Latest Mutation Signatures Assigns signatures to samples

To run the SigProfiler software, you will have to activate an environment (mutational_signatures), What is an Environment?

An environment is an isolated space where specific software, dependencies, and libraries are installed. It ensures that all required tools run in a controlled and reproducible way, avoiding conflicts with other system applications.

For this course, we use the mutational_signatures and samtools_env environment.

⚠️ Note: Software will not work outside the environment.

How to Activate the mutational_signatures Environment

Before using any software, activate the environment with:

conda activate mutational_signatures

How to Activate the samtools_env Environment

Before using any software, activate the environment with:

conda activate samtools_env

To deactivate the environment when you're done:

conda deactivate

Link to mutational_signatures.yml Installation Guide here SigProfilerHelper

Informatics Set-Up

For installation and setup, please refer to the following guides:

  • Oracle VM VirtualBox Installation Guide – Detailed instructions for installing and configuring VirtualBox on different operating systems. (Note: Separate installations are needed for Intel-based and ARM-based Macs, and the VDI files will differ.)

The Host Operating System Requirements are:

  • RAM requirement: 8GB (preferably 12GB)
  • Processor requirement: 4 processors (preferably 8)
  • Hard disk space: 200GB
  • Admin rights to the computer

Citing and Reusing Course Material

The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Creative Commons Licence

Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.

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