README

FrangiPANe is a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach. It was previously developed as a modular and interactive application based on Jupyter Book.

It has now been recoded and integrated into a Snakemake pipeline.

How to install FrangiPANe ?

Requirement

You have to install :

• git (https://git-scm.com/)
• singularity (https://...)

Clone the git repository

git clone https://forge.ird.fr/diade/frangipane.git

Install the frangiPANe python package

cd PATH_2_FRANGIPANE_DIRECTORY
python3 -m pip install -U pip setuptools build
python3 -m pip install -e .

Updating snakecdysis package (ref) using by frangiPANe

python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main

Install frangiPANe tool in a cluster mode

frangiPANe install_cluster -s slurm -e singularity

sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh

Download singularity container

wget ...

Checking if frangiPANe has been correctly installed

frangiPANe

Run FrangiPANe

Download a dataset to test frangiPANe

frangiPANe test_install -d ../../data/

Authors

For version 2.0: Sebastien Ravel and Christine Tranchant-Dubreuil (2024).

Previous versions

0.1: Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013.

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 Sebastien Ravel and Christine Tranchant-Dubreuil
• Copyright 2024