InfoGenomeR

• InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific CNAs, and haplotype information to identify the optimal breakpoint graph representing cancer genomes.

Snakemake install

• The InfoGenomeR workflow is run by the snakemake.
• Environments are described in workflow/envs.
• Rules are described in workflow/Snakefile.

  wget https://github.com/conda-forge/miniforge/releases/download/24.1.2-0/Miniforge3-Linux-x86_64.sh
  bash Miniforge3-Linux-x86_64.sh
  mamba create -c conda-forge -c bioconda -n snakemake snakemake
  conda config --set channel_priority strict
  conda activate snakemake

  InfoGenomeR repository

  git clone https://github.com/dmcblab/InfoGenomeR.git
  InfoGenomeR_repo=${PWD}/InfoGenomeR

  After git clone, follow the steps below.

• Conda environment setting
• Dataset download
• InfoGenomeR workflow

Conda environment setting

snakemake --core all --use-conda InfoGenomeR_env

Dataset download

snakemake --cores all --use-conda InfoGenomeR_download

InfoGenomeR workflow

Take a low coverage example (~50G). Check the example is working, and then replace example files with yours.

snakemake --core all --use-conda InfoGenomeR_example_download

Make a workspace

# go to the InfoGenomeR repository.
cd ${InfoGenomeR_repo}

# make a workspace directory
workspace_dir=InfoGenomeR_workspace1
mkdir -p ${workspace_dir}

# link the reference in the workspace directory
ln -s ${PWD}/humandb/ref ${workspace_dir}/ref

Starting from fastq

Take the low coverage example in examples/fastq

Inputs should be located in the workspace

• fastq/normal1.fq.gz (optional for somatic)
• fastq/normal2.fq.gz (optional for somatic)
• fastq/tumor1.fq.gz
• fastq/tumor2.fq.gz

  ln -s ${PWD}/examples/fastq ${workspace_dir}/fastq

  Then, go to InfoGenomeR run

  Starting from bam

  Inputs should be located in the workspace

  If you start here, the bam folder would be yours, where the bam files should be named as below.

• bam/normal_sorted.bam (optional for somatic)
• bam/tumor_sorted.bam

  ln -s bam ${workspace_dir}/bam

  Then, go to InfoGenomeR run

  InfoGenomeR run

  Select either somatic (if a matched normal exists) or total (all variants in tumor) mode

  Somatic run

  # Run the InfoGenomeR workflow. The example is triploidy
  snakemake --core all --use-conda ${workspace_dir}/InfoGenomeR_output --config mode=somatic min_ploidy=2.5 max_ploidy=3.5 

  Total run

  snakemake --core all --use-conda ${workspace_dir}/InfoGenomeR_output --config mode=total min_ploidy=2.5 max_ploidy=3.5