GenoPath

Developers: Ryan Tobin, Sayaka Miura, Sudhir Kumar
Institute: Institute for Genomics and Evolutionary Medicine, Temple University

Introduction

GenoPath is a genomic analysis pipeline that combines efficiency and user-friendliness to ease tumor evolution analysis. It integrates cutting-edge bioinformatics tools for predicting clones, inferring cell migration routes, and more. You can download the manual by clicking here Manual.

Installation

System Requirements

• Operating System: Windows
• Python: 3.11
• R: 4.3.0
• Java
• MegaCC (Download available from http://www.megasoftware.net)
• Anaconda or Miniconda (recommended)

Steps

1. Clone the repository:

   git clone https://github.com/ryan-tobin/GenoPath
   cd GenoPath

2. Set up the environment using Anaconda or Miniconda:

   conda create -n genopath python=3.11
   conda activate genopath

3. Install required libraries and dependencies:

   pip install -r requirements.txt

Getting Started

Running GenoPath

To run GenoPath with the provided sample dataset. Navigate to where you downloaded GenoPath and use the files located in the Sample_Datasets folder:

python genopath.py --run_process All --target_dir [path/to/dir] snv Sample_Datasets/input.tsv --max_graphs_per_tree 50 --control_file Sample_Datasets/control.txt --abundance_weighted True --sv_file Sample_Datasets/sv.txt

Pipeline Components

CloneFinder

• Purpose: Infers tumor cell population genotypes from bulk sequencing data.
• Usage:

  python genopath.py --run_process CloneFinder --target_dir [path/to/dir] snv [path/to/input.tsv]

PathFinder

• Purpose: Reconstructs cancer cell migration routes.
• Usage:

  python genopath.py --run_process CloneFinder PathFinder --target_dir [path/to/dir] snv [path/to/input.tsv] --primary [tumor] --max_graphs_per_tree [int]

PhyloSignare

• Purpose: Detects branch-specific mutation signatures.
• Usage:

  # With Known Driver Mutations
  python genopath.py --run_process CloneFinder PhyloSignare --target_dir [path/to/dir] --driver_mutation_file [path/to/file] snv [path/to/input.tsv] [path/to/control_file]
  
  # With Driver Mutation Calculation
  python genopath.py --run_process CloneFinder PhyloSignare --target_dir [path/to/dir] --ref_alt_file [path/to/file] --tool CGI --email [email] --token [token] --cancer_type_input [cancer_type] snv [path/to/input.tsv] [path/to/control_file]
  
  # No Driver Mutation Analysis
  python genopath.py --run_process CloneFinder PhyloSignare --target_dir [path/to/dir] snv [path/to/input.tsv] [path/to/control_file]

Picante

• Purpose: Analyzes phylogenetic diversity and community structure.
• Usage:

  # Picante (All)
  python genopath.py --run_process CloneFinder Picante_all --target_dir [path/to/dir] snv [path/to/input.tsv] --abundance_weighted [True/False]
  # Picante (Comdist)
  python genopath.py --run_process CloneFinder Picante_comdist --target_dir [path/to/dir] snv [path/to/input.tsv] --abundance_weighted [True/False]
  # Picante (Comdistnt)
  python genopath.py --run_process CloneFinder Picante_comdistnt --target_dir [path/to/dir] snv [path/to/input.tsv] --abundance_weighted [True/False]
  # Picante (Unifrac)
  python genopath.py --run_process CloneFinder Picante_unifrac --target_dir [path/to/dir] snv [path/to/input.tsv] --abundance_weighted [True/False]

Meltos

• Purpose: Constructs tumor phylogeny trees based on structural variants.
• Usage:

  python genopath.py --run_process CloneFinder Meltos --target_dir [path/to/dir] snv [path/to/input.tsv] --sv_file [path/to/sv_file]

Driver Mutation Analysis

• Purpose: Identifies driver mutations in tumor sites. NOTE Meltos is not run with the All function and must be run separately.
• Usage:

  # Calculating Driver Mutations
  python genopath.py --run_process All --target_dir [path/to/dir] --ref_alt_file [path/to/file] --tool CGI --email [email] --token [token] --cancer_type_input [cancer_type] snv [path/to/input.tsv]
  
  # Known Driver Mutations
  python genopath.py --run_process All --target_dir [path/to/dir] --driver_mutation_file [path/to/file] snv [path/to/input.tsv]
  
  # No Driver Mutation Analysis
  python genopath.py --run_process All --target_dir [path/to/dir] snv [path/to/input.tsv]

• With OpenCRAVAT

  python driver_mutations_with_cravat.py -i [/path/to/input] -o [/path/to/output] -c [cancer_type ]

Output Files

Output files will be generated in the specified target directory.

License

This project is licensed under the BSD-3 License - see the LICENSE file for details.

Acknowledgments

GenoPath development is supported by the Institute for Genomics and Evolutionary Medicine at Temple University.