nanopore_simulation: A Python repository from crohrandt

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

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 ./

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

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.

DNA-Example

Simulate human DNA reads

cd examples
cd DNA
./DNA_quick_example_run.sh

./DNA_full_example_run.sh

Basecall simulated Fast5s with albacore 2.1.1

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

Map basecalled reads with minimap 2.1

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

Tested with

ONT albacore 2.1.1
minimap2 2.11-r311