The NGS_Workflows repository, is a collection of workflows and scripts designed for Next-Generation Sequencing (NGS) data analysis. It encompasses various tools and pipelines to facilitate the processing and interpretation of NGS data.

Repository Structure

The repository is organized into several directories, each focusing on different aspects of NGS data analysis:

• Fastq-manipulation-in-R-main: Contains R scripts for handling and processing FASTQ files, which are commonly used in NGS data.

• Nextflow: Includes workflows developed using Nextflow, a workflow management system that enables scalable and reproducible scientific workflows.

• Pathway-Analysis-Tool-main: Offers tools for conducting pathway analysis, aiding in the interpretation of biological pathways from NGS data.

• RNASeq-DESEq2-main: Provides scripts and workflows for RNA-Seq data analysis using DESeq2, a tool for differential gene expression analysis.

• Single_Cell: Contains resources and workflows tailored for single-cell sequencing data analysis.

• Snakemake-Workflow-Template-master: Offers templates for creating workflows using Snakemake, a workflow management system that simplifies the creation of complex data analysis pipelines.

• Spatial_Transcriptomics-main: Includes tools and scripts for spatial transcriptomics, a technique that combines spatial information with gene expression data.

• WholeExomeSequencing-Pipeline-main: Provides a pipeline for whole-exome sequencing data analysis, facilitating the identification of genetic variants.

• shraq-main: Contains additional scripts and tools related to NGS data analysis.

Getting Started

To explore the contents of this repository:

1. Clone the Repository:

   git clone https://github.com/pritampanda15/NGS_Workflows.git

2. Navigate to a Directory:

   cd NGS_Workflows/Nextflow

3. Review Documentation: Each directory may contain its own README or documentation detailing installation steps, dependencies, and usage instructions.

Contributing

Contributions to enhance the repository are welcome. To contribute:

1. Fork the Repository: Click on the 'Fork' button at the top right corner of the repository page.

2. Create a New Branch: For your feature or bug fix.

   git checkout -b feature-name

3. Make Changes: Implement your feature or fix.

4. Commit Changes:

   git commit -m "Description of changes"

5. Push to Your Fork:

   git push origin feature-name

6. Submit a Pull Request: Navigate to your forked repository on GitHub and click on 'New Pull Request'.

License

The repository does not specify a license. It's advisable to contact the repository owner for clarification before using the code in commercial or open-source projects.

For more details, visit the NGS_Workflows repository.