SNS-EXT: Seq-N-Slide Extended for Minerva HPC

A specialized adaptation of the Seq-N-Slide (SNS) pipeline optimized for Mount Sinai's Minerva High Performance Computing (HPC) environment with LSF job scheduling.

Overview

SNS-EXT provides automated workflows for common Illumina sequencing-based protocols, including:

• RNA-seq: Differential gene expression analysis
• ChIP-seq: Chromatin immunoprecipitation sequencing
• ATAC-seq: Assay for transposase-accessible chromatin
• WGBS/RRBS: Whole genome and reduced representation bisulfite sequencing
• WES/WGS: Whole exome/genome variant detection
• Species identification: Contaminant screening and quality control

Key Features

• ✅ Minerva-optimized: Configured for LSF job scheduler and Minerva-specific resources
• ✅ Modular design: Individual segments for flexible workflow construction
• ✅ Quality control: Comprehensive QC metrics and reporting
• ✅ Standardized outputs: Consistent file formats and directory structures
• ✅ Resource management: Optimized memory and CPU allocation for HPC environment

Installation

```bash

Clone the repository

git clone https://github.com/Naiklab/sns-ext.git cd sns-ext

Make scripts executable

chmod +x run generate-settings gather-fastqs chmod +x routes/.sh chmod +x segments/.sh chmod +x scripts/*.sh ```

Quick Start

1. Generate project settings:

bash ./generate-settings

1. Gather FASTQ files:

bash ./gather-fastqs /path/to/fastq/directory

1. Run analysis pipeline:

bash ./run [route] [sample-name]

Available Routes

| Route | Description | |-------|-------------| | rna-star | RNA-seq with STAR alignment | | rna-salmon | RNA-seq with Salmon quantification | | rna-rsem | RNA-seq with RSEM quantification | | chip | ChIP-seq analysis | | atac | ATAC-seq analysis | | wgbs | Whole genome bisulfite sequencing | | rrbs | Reduced representation bisulfite sequencing | | wes | Whole exome sequencing | | species | Species identification and contamination screening |

Directory Structure

text sns-ext/ ├── routes/ # Main analysis workflows ├── segments/ # Individual processing steps ├── scripts/ # Utility and analysis scripts ├── run # Main execution script ├── generate-settings # Project configuration utility └── gather-fastqs # FASTQ file organization utility

Configuration

The pipeline uses a settings file to configure analysis parameters. Key settings include:

• Reference genome paths
• Tool-specific parameters
• Resource allocation (memory, CPU)
• Output directory structure

Dependencies

• LSF job scheduler (Minerva HPC)
• Standard bioinformatics tools (STAR, Salmon, MACS2, etc.)
• R with required packages
• Python with necessary libraries

Original SNS Pipeline

This project is based on the original Seq-N-Slide pipeline:

GitHub: igordot/sns
Documentation: https://igordot.github.io/sns
DOI:

Citation

If you use SNS-EXT in your research, please cite both this adaptation and the original SNS pipeline.

License

See LICENSE file for details.

Support

For issues specific to the Minerva adaptation, please open an issue in this repository. For general SNS questions, refer to the original documentation.