The Mystery of Parasites

"The Mystery of Parasites" is a computational biology project aimed at uncovering the genomic secrets of various parasitic species. Utilizing a series of bioinformatic tools and workflows, this project analyzes genomic sequences to identify tRNA genes, ribosomal RNA genes, and repeats, alongside conducting BLAST searches for comparative genomics studies.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

What things you need to install the software and how to install them:

• Snakemake
• Conda

Installing

A step-by-step series of examples that tell you how to get a development environment running:

1. Clone the repository to your local machine:

git clone https://github.com/pinaryildiz/TheMysteryOfParasites.git

Dependencies

To run the analysis, you will need Conda installed on your system. If you do not have Conda, please follow the official installation guide.

Once Conda is set up, you can create an environment with all the necessary dependencies using the provided env.yaml file. This environment includes tools such as tRNAscan-SE, Barrnap, RepeatMasker, RepeatModeler, BLAST, OrthoFinder, and several Python packages for data manipulation and visualization.

To create and activate the environment, run:

conda env create -f env.yaml
conda activate TheMysteryOfParasites

Setting Up the Workflow

1. tRNAscan: Identifies tRNA genes within the genomic sequences of specified parasites.
2. Barrnap: Searches for ribosomal RNA genes, providing insights into the genomic structure related to the organisms' protein synthesis machinery.
3. Make BLAST Database: Prepares a BLAST database from the genomic sequences, enabling rapid sequence similarity searches.
4. BLAST Search: Performs BLAST searches against the prepared database to find similar sequences across different organisms.
5. Repeat Analysis: Uses RepeatMasker and RepeatModeler to identify and analyze repeat sequences within the genomes, crucial for understanding genomic evolution and structure.

Workflow Execution

To execute the workflow, ensure that you have all the necessary input files in the resource/Genome/ directory. Then, from the root of your project directory, run:

snakemake --use-conda

This command will execute the workflow as defined in the Snakefile, processing each rule based on the dependencies and inputs specified.

Contributors

• Pınar YILDIZ - All projects

Acknowledgments

• Mention any collaborators, funding agencies, or anyone else who supported the project.