/nanopore_simulation

Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore Technologies MinION device for bioinformatic development.

Primary LanguagePythonMozilla Public License 2.0MPL-2.0

Nanopore SimulatION

Inputs Outputs
Configuration-File (derived form a real conducted experiment)
Reference genome FASTA-File (may be from another species) Basecallable Fast5-Files with raw values
Model-File (provided by ONT)

Description

Nanopore SimulatION is a tool for simulating an Oxford Nanopore Technologies MinION device for bioinformatic development.

Installation

Install the Nanopore SimulatION package:

conda create -n Simulator python=3
conda activate Simulator
git clone ssh://git@192.168.224.185:7999/~liubiao2/simulator.git
cd simulator
pip install -e ./
Dependencies

All dependencies should be automatically installed by pip.

Installation
  • numpy
  • scipy
  • biopython
  • argparse
  • pandas
  • h5py
  • matplotlib (for future use, yet only pylab is used)

Usage

Examples

DNA-Example

Simulate human DNA reads
cd examples/DNA
./Simulator.sh