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