This repository contains tools and workflows for processing and analyzing single-cell data generated with Oxford Nanopore Technologies (ONT). It is designed to support high-throughput analysis pipelines and flexible exploration of single-cell transcriptomic data.
- Snakemake Workflow: Automates data processing using a customizable pipeline defined in
Snakefile. - Conda Environment: Pre-configured environment setup for reproducible analyses.
- Scripts and Utilities: Includes helper scripts for specific tasks like data formatting, cluster configuration, and runtime management.
- Resource Management: SLURM-based launcher script for efficient use of computational resources.
config/: Configuration files for Snakemake workflows.envs/: Conda environment specifications.notebooks/: Jupyter Notebooks for exploratory data analysis.resources/: Additional resources and reference data.rules/: Snakemake rule definitions.scripts/: Custom scripts used throughout the pipeline.utils/: Utility functions and helper tools.workflow.smk: The main workflow file for Snakemake.