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ONT-Single-Cell

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.

Features

  • 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.

Repository Structure

  • 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.