frangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assembly approach. It consists in a Jupyter Notebook application that centralizes code,documentation and interactive visualizations together

It is available as a Docker image that contains (i) a jupypter notebook centralizing code, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software (XXX)needed for each step of the analysis.

Requirements

• Docker : https://docs.docker.com/get-docker/

• Python3 (v3.9.7) : https://www.python.org/

• biopython : https://biopython.org/

• panel : https://panel.holoviz.org/

• abyss : https://github.com/bcgsc/abyss/blob/master/README.md

• bwa (v. 0.7.17) : https://github.com/lh3/bwa/blob/master/README.md

• ea-utils (fastq-stats, v 1.01) : https://expressionanalysis.github.io/ea-utils/

• samtools (v1.10) : http://www.htslib.org/

• assembly-stats : https://github.com/sanger-pathogens/assembly-stats

• cd-hit : https://github.com/weizhongli/cdhit/blob/master/README

How to use FrangiPANe ?

On our computer (linux or mac OS)

You have to install git (https://git-scm.com/) and docker (https://docs.docker.com/get-docker/) on your computer.

Clone the git repository

git clone https://github.com/tranchant/frangiPANe.git

Build the docker machine

After installing Docker, build the docker machine. FrangiPANe uses jupyter/datascience-notebook (more information : https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html)

sudo docker build -t frangipane .

Run FrangiPANe

• Download a dataset to test frangiPANe

wget https://itrop.ird.fr/frangiPANe/data_test.tar.gz
tar zxvf data_test.tar.gz

NOTE on disk space required: once the directory is unzipped, the size of the test data directory is approximately 3.4 GB and frangiPANe will generate approximately 7.6 GB of data. Thus, 11 GB of disk space is required to use frangiPANe with the downloaded dataset.

• Launch the docker virtual machine with the command docker run. You can connect a local directory to your frangiPANe docker container by using the option -v. So, for example, specify the directory path for the decompressed directory that contains the dataset tot test frangiPANe.

docker run -u $(id -u) -v /local/path/2/DATA:/mydata -p 10001:8888 frangipane:latest

NOTE : The command just above starts a container running a Jupyter Notebook server and exposes the server on host port 10001. The server logs appear in the terminal and include a URL to the notebook server, but with the internal container port (8888) instead of the correct host port (10001).

Around the end of the outputs, you can find the URL with a token. You can :

• copy the url to open it in your default web browser. You have to change the port from 8888 to 10001 if you use the option -p 10001:8888

• or open the following link in your your default web browser: http://127.0.0.1:10001/lab and enter the token to lanch jupyter lab and frangiPANe notebook.

• From the homepage for jupyter notebook, open the directory frangiPANe then open the jupyter book frangiPANe.ipynb

• Once the book opened, execute each notebook's cell.

Nb : If you have connected your docker machine to the local directory with the downloaded dataset as described above, you can test frangiPANe by filling out the form as described below:

Licence

• Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and GPLv3

• Intellectual property belongs to IRD/UMR DIADE.

• Written by Clothilde Chenal and Christine Tranchant-Dubreuil

• Copyright 2021