SDgenerator v2

SDgenerator is a python program to create synthetic samples (in FASTQ format) with a controled population of DVGs (proportion & type)

The version 2 consider the case that all the genomes in the sample doesn't have to share a common genomic coordinate (@jmusan).

Table of Contents

1. About The Project
   • External Program
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Contact
5. Acknowledgements

Third party program

wgsim (reads simulator)

https://github.com/lh3/wgsim

Getting Started

To get a local copy up and running follow these simple steps.

Installation

1. Clone the repo in the directory of your choice

   git clone https://github.com/MJmaolu/SDgenerator.git

2. Go to the DVGfinder directory

   cd SDgenerator

3. Give execution permission to all the scripts in the SDgenerator directory

   chmod -R +x .

4. Create a new environment with conda with all the dependencies needed to run SDgenerator

   conda env create -f sdgenerator_env.yaml

5. Activate SDgenerator environment

   conda activate sdgenerator_env

Usage

python3 SDgenerator.py -t population_csv -N number_total_reads [-l length_reads. Default 100] -o output_basename [-d outer_distance. Default 300]

Input formats

Population_csv example

BP,RI,DVG_type,proportion
6194,8961,Deletion_forward,0.1
23000,120,Deletion_reverse,0.1
9478,9489,3cb/sb,0.1
10000,9800,5cb/sb,0.1
2200,2100,Insertion_forward,0.1
1000,1200,Insertion_reverse,0.1

The proportion of the wild type genome is calculated as the substraction to 1 of the sum of the DVG proportions

Supported DVG types

• Deletion_forward

• Deletion_reverse

• 3cb/sb

• 5cb/sb

• Insertion_forward

• Insertion_reverse

Contact

María José Olmo-Uceda - maolu@alumni.uv.es

PhD student

EvolSysVir Group, I²SysBio (CSIC-UV)