cpgonzal/nanodj repository overview

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

⁠Run NanoDJ container:

Clone the repository and pull the image from Dockerhub (recommended):

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

*The NanoDJ image can be also built locally using 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.

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:

• 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:

• https://github.com/nanopore-wgs-consortium/NA12878/blob/master/Genome.md⁠

Porechop notebook data:

• https://github.com/rrwick/Porechop/files/901044/1_out.fastq.zip⁠

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

• To be released.

⁠NanoDJ support:

Feel free to open a new issue on this repository or contact us by email: [email protected]⁠

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

⁠How to cite NanoDJ:

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.

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