BiaoLiu2017 / nanopore_simulation

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

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