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NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly
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README.md

Binder VICE

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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.

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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.

This project is now integrated in VICE, a visual and interactive computing environment which is part of CyVerse, a project that consist of platforms, tools and services built in order to provide life scientists with powerful computational infrastructure to handle huge datasets and complex analyses.

NanoDJ has been tested using a clean Ubuntu virtual machine only with Docker v1.13.1 installed

Run NanoDJ container:

Clone the repository and pull the image from Docker Hub (recommended):

git clone https://github.com/genomicsITER/NanoDJ.git
cd NanoDJ
docker pull genomicsiter/nanodj:latest

*The NanoDJ image can be also built locally using docker build -t genomicsiter/nanodj:latest .

Create a container with the image:

docker run -it --rm -p 8888:8888 -v /path/to/nanodjrepo/nanodj_notebooks:/home/jovyan/notebooks genomicsiter/nanodj:latest

In order to spawn the Bandage GUI from NanoDJ on your machine, you should run the container setting the DISPLAY environment variable and mounting the X11 socket as shown below. This is only valid for Linux users:

docker run -it --rm -p 8888:8888 \  
           -e DISPLAY=$DISPLAY \  
           -v /tmp/.X11-unix:/tmp/.X11-unix \  
           -v /path/to/NanoDJ/nanodj_notebooks:/home/jovyan/notebooks \  
           genomicsiter/nanodj:latest

After running the docker run command, 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.

Write permission on notebook files

Files and directories mounted as a volume doesn't have the UID and GID of the container's user (jovyan) so changes in notebooks can't be saved. You should change the owner of the mounted files with this command on your host machine after cloning the repository.

sudo chown -R 1000:100 ./nanodj_notebooks

With this command we change the owner recursively setting the UID and GID with the jovyan user values.

Additional data

Escherichia coli data links:

Human DNA mitochondrial data:

Porechop notebook data:

Streptococcus agalactiae Illumina reads (PE300) and R9.0 SpotON FAST5 files:

Getting help with NanoDJ

Feel free to open a new issue on this repository or contact us by email: genomica@iter.es

How to cite NanoDJ:

Rodríguez-Pérez H, Hernández-Beeftink T, Lorenzo-Salazar JM, Roda-García JL, Pérez-González CJ, Colebrook M, Flores C. NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly. BMC Bioinformatics (2019 20:234) https://doi.org/10.1186/s12859-019-2860-z

Funding:

This research was funded by the Instituto de Salud Carlos III (grants PI14/00844 and PI17/00610), the Spanish Ministry of Science, Innovation and Universities (grant RTC-2017-6471-1; MINECO/AEI/FEDER, UE), the Spanish Ministry of Economy and Competitiveness (grant MTM2016-74877-P), which were co-financed by the European Regional Development Funds ‘A way of making Europe’ from the European Union, and by the agreement OA17/008 with Instituto Tecnológico y de Energías Renovables (ITER) to strengthen scientific and technological education, training, research, development and innovation in Genomics, Personalized Medicine and Biotechnology.

NanoDJ image logo by Daniel Medina (IG:@danymedale)

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