NanoDJ is a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.
NanoDJ is built as a Docker container that runs a Jupyter Lab instance. The user can work with ONT data using the notebooks that are provided or open a new Jupyter Lab session and run the included software packages.
NanoDJ has been tested using a clean Ubuntu virtual machine only with Docker v1.13.1 installed
Clone the repository and build the image locally (soon on Dockerhub):
git clone https://github.com/genomicsITER/NanoDJ.git
cd NanoDJ
docker build -t nanodj:latest .
Create a container with the image:
docker run -it --rm -p 8888:8888 -v /path/to/nanodjrepo/nanodj_notebooks:/home/jovyan/notebooks nanodj:latest
Open the localhost:8888/token link that appears in the output after the Jupyter Lab instance is started.
NanoDJ includes data and notebooks. However, a volume (the -v option) should be created to import these materials. With this volume, input and output data and modified notebooks can be saved on your host machine.
Mac users
Notebooks directory must be added in the Docker GUI options (on file sharing section) before mounting that directory. Once it is in the list, volume should be mounted with the -v option as usual.
Windows users
Check that the directory that is going to be mounted is under the C:\Users directory. This path is written as "/c/Users/" in the -v option.
On Windows 8.1, the Jupyter Lab instance cannot be accessed from localhost:8888/lab. "localhost" must be replaced with the IP of the VM that runs Docker on your system.
Escherichia coli data links:
- 1D: https://s3.climb.ac.uk/nanopore/E_coli_K12_1D_R9.2_SpotON_2.tgz
- 2D: https://s3.climb.ac.uk/nanopore/R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.tar
Human DNA mitochondrial data:
Porechop notebook data:
Streptococcus agalactiae Illumina reads (PE300) and R9.0 SpotON FAST5 files:
- To be released.
Feel free to open a new issue on this repository or contact us by email: genomica@iter.es
Rodríguez-Pérez H, Hernández-Beeftink T, Lorenzo-Salazar JM, Roda-García JL, Pérez-González CJ, Colebrook M, Flores C. (2018) NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly. Submitted.