Welcome to AsaruSim

AsaruSim is an automated Nextflow workflow designed for simulating 10x single-cell Nanopore reads. It allows to benchmark and optimize single-cell Nanopore long read data processing pipelines.

Github repository AsaruSim.

Requirements

  • Nextflow - A workflow engine for complex data pipelines.
  • Docker or Singularity - Containers for packaging necessary software, ensuring reproducibility.

Install nextflow

Ensure you have the following installed on your system:

Java 8 or later: Nextflow requires Java. Install it from Oracle or use a package manager like apt, brew, or yum depending on your OS.

curl -s https://get.nextflow.io | bash
chmod +x nextflow
sudo mv nextflow /usr/local/bin/

Nextflow is now installed and ready to use on your system. For further details on using Nextflow, refer to the official documentation.

Install docker

Install Docker.

Run AsaruSim

  • 1 - Clone the github repository
git clone https://github.com/alihamraoui/AsaruSim.git

cd AsaruSim
  • 2 - Run using nextflow
nextflow run main.nf --help