Bioinfo Scripts

A collection of bioinformatics workflows analysis on local machines and HPC clusters.

🔧 Workflows

inStrain Pairwise Comparison Pipeline

Location: snakefiles/inStrain_compare/

A flexible Snakemake pipeline for automated pairwise comparisons of inStrain microbial strain profiles. Supports three comparison modes:

• Type Mode: Compare samples by category (e.g., gut vs skin microbiomes)
• Path Mode: Compare all profiles within specified directories
• Profile Mode: Direct comparison of specific profile pairs

Key Features:

• 🔄 Three flexible input modes for different use cases
• 🚀 Parallel execution on HPC clusters (SLURM)
• 📊 Automated resource management
• 🗂️ Organized output structure
• ⚙️ Configurable inStrain parameters

View detailed documentation →

🚀 Quick Start

Prerequisites

• Snakemake (≥7.0)
• Conda/Mamba for environment management
• Python packages: pandas

Local Execution

# Clone the repository
git clone https://github.com/Sidduppal/bioinfo-scripts.git
cd bioinfo-scripts

# Navigate to a workflow
cd snakefiles/inStrain_compare

# Configure your analysis
vim config.yaml

# Test the workflow
snakemake -n

# Run locally
snakemake --cores 8

Cluster Execution

For SLURM clusters, use the provided Snakemake profile:

# Test cluster submission
snakemake -s <snakefile.smk> --profile ../profile -n

# Submit to cluster
snakemake -s <snakefile.smk> --profile ../profile

The profile automatically handles:

• Job submission and queuing
• Resource allocation (CPU, memory, time)
• Log file organization
• Job failure handling and retries

📁 Repository Structure

bioinfo-scripts/
├── README.md                          # This file
├── LICENSE                            # GPL-3.0 license
├── snakefiles/                        # Snakemake workflows
│   ├── profile/                       # SLURM cluster profile
│   │   └── config.yaml               # Cluster execution settings
│   └── inStrain_compare/             # inStrain comparison pipeline
│       ├── README.md                 # Pipeline documentation
│       ├── config.yaml               # Pipeline configuration
│       └── inStrain_compare_parallel.smk  # Main Snakefile
└── .gitignore                        # Git ignore patterns