Simulation of Virus Detection in CHO Cells for Oxford Nanopore Sequencing Using Hypergeometric Probability

Project Description

This repository implements the research paper by Roushangar et al. that covers the work for simulating virus detection using hypergeometric probability for Oxford Nanopore sequencing.

Directory Structure

src: Contains source code files and a detailed README.md describing each script and its functions.
FeLV_24Threads_YES10%ReadPercentError_10power2VirusHostRatio_Simulation3: Simulation data directory.
MVM_24Threads_YES10%ReadPercentError_10power2VirusHostRatio_Simulation3: Simulation data directory.
PCV1_24Threads_YES10%ReadPercentError_10power2VirusHostRatio_Simulation3: Simulation data directory.
ons_simulation_main.py: Main script to run the simulation.
submit.sh: Script for submitting jobs.
requirements.txt: List of required Python packages.

System Requirements

macOS 10.15 or higher / Windows 10 or higher / Linux
Python 3.10.6
BLAST+ 2.13.0
*May work with similar versions.

Dependencies

pandas >= 1.5.1
biopython >= 1.79

Installation Instructions

Clone the repository:

git clone https://github.com/raeufroushangar/ONS_virus_detection_simulation.git
cd ONS_virus_detection_simulation

Create a virtual environment inside the ONS_virus_detection_simulation directory:
```
python3 -m venv venv
```
Activate the virtual environment:
- On macOS and Linux:
```
source venv/bin/activate
```
- On Windows:
```
 .\venv\Scripts\activate
```
Install required packages:
```
pip install -r requirements.txt
```

Run the analysis script:

python3 ons_simulation_main.py MVM 'Minute virus of mice.fasta' 50 'GCF_000223135.1_CriGri_1.0_genomic.fna' 1 '/path/to/refSeq' 10power2 50 500 yes 10 24 3

Explanation of Inputs:

MVM: Virus symbol (e.g., MVM for Minute Virus of Mice)
'Minute virus of mice.fasta': Virus reference genome file name
50: Number of virus genomes to use
'GCF_000223135.1_CriGri_1.0_genomic.fna': Host reference genome file name
1: Number of host genomes to use
'/path/to/refSeq': Reference genome directory path
10power2: Virus to host ratio string to add to the output file name
50: Minimum read length
500: Maximum read length
yes: Error status (Yes/No)
10: Sequencing read error percentage
24: Number of logical threads to use
3: Simulation number

Replace the paths and parameters with those suitable for your environment and data.