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

For Debian-based distros (Debian, Ubuntu, Linux Mint) install:

sudo apt-get install python3-tk

For CentOS, Redhat Linux install:

sudo yum install python3-tkinter

After that, install the Nanopore SimulatION package:

git clone https://github.com/crohrandt/nanopore_simulation
cd nanopore_simulation
pip3 install -e ./

All dependencies should be automatically installed by pip.

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

In the examples directory several standard use cases will be predefined for quick usage. Each use case is structured within an own subdirectory. To try out the examples the bash-script needs to be run. Every file that is requireed is packaged or will be downloaded from a free and open source download site.

For the complete verification, a pipeline is described using the ONT albacore basecaller in version 2.1.1 and a mapping of the simulated reads to the reference genome using minimap2 in version 2.1-r311.

cd examples
cd DNA
./DNA_quick_example_run.sh

or

./DNA_full_example_run.sh

cd Run-Output
read_fast5_basecaller.py -i . -o fast5,fastq -s basecalled -f FLO-MIN106 -k SQK-LSK108 -t 4 -r

minimap2 -ax map-ont ../../Homo_sapiens.GRCh38.dna.primary_assembly.fa basecalled/workspace/pass/*.fastq > Run-Output.sam

• ONT albacore 2.1.1
• minimap2 2.11-r311