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Last pushed: 2 months ago
Short Description
Super Easy Simulation of Genomic Variations
Full Description

VarSimLab is a Docker-based package that is designed to study genomic variations in a given genome. As of the current version (nabavilab/varsimlab:0.0.2), the simulator generates artificial short reads, which harbor structural and copy number variations. In addition, it simulates tumor heterozygosity (Ploidy and Subclones).

With a web-based interface running locally, it not only provides a convenient way of using the package, but also runs efficiently generating data where it will be finally analyzed.

Prepare The Reference Genome

There are two ways to easily run VarSimLab for a reference genome

To prepare a reference genome, follow these steps:

  1. Create a new folder to hold your files.
  2. Copy the reference genome in FASTA format (.FASTA | .FA ) to the folder. You can also download genome from UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgGateway
  3. Create a text file and name it manifest.json. Put the following text after replacing the values of the keys with the name of the files you just copied. Save the file and close it.
    {
     "reference": "reference.fa"
    }
    
    That’s it! Your reference is ready to generate reads from

Running VarSimLab

docker run -v $(pwd):/ref -p 31331:8000 nabavilab/varsimlab

The -v option mounts the current folder to the container, where the pipeline will check for the reference files. The -p mounts links port 8000 from the container to port 31331 on you local machine (you can choose other ports too). Now, naviate to the web browser to http://localhost:31331

Full Documentation

http://varsimlab.readthedocs.io/en/latest/

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Owner
nabavilab