README.rst

FrangiPANe

a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.

Previously developed as a modular and interactive application based on Jupyter Book [1] , it has now been recoded and integrated into a Snakemake pipeline.

I - Installing FrangiPANe

1.1 - Install the frangiPANe python package

Requirement

• Git
• Singularity

Clone the git repository

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

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

NOTE : Updating snakecdysis package (ref) using by frangiPANe if necessary

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

1.2 Install frangiPANe tool

Choose only one mode

• in a cluster mode

frangiPANe install_cluster -s slurm -e singularity

• or in local mode

frangiPANe install_local

Add the prompt complementation

sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh

Download or build the singularity container in the container directory

# Download the container
wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
# OR build the container
singularity build frangiPANe.sif frangiPANe.def

Checking if frangiPANe has been correctly installed

frangiPANe

FrangiPANe structure

frangipane
├── docs
│   ├── build
│   ├── requirements.txt
│   └── source
├── frangiPANe
│   ├── containers
│   │   ├── frangiPANe.def
│   │   └── frangiPANe.sif
│   ├── default_profile
│   │   ├── cluster_config.yaml
│   │   ├── config.yaml
│   │   └── ...
│   ├── frangiPANe-complete.sh
│   ├── install_files
│   │   ├── cluster_config_SLURM.yaml
│   │   ├── config.yaml
│   │   └── tools_path.yaml
│   ├── main.py
│   ├── module.py
│   ├── report
│   ├── schemas
│   ├── snakefiles
│   ├── snakemake_scripts
│   │   ├── frangiPANe.py
│   │   ├── generate_jb_frangiPANe.py
│   │   ├── generate_jb.py
│   │   └── __init__.py
│   └── VERSION
├── LICENSE
├── pyproject.toml
└── README.rst

II - Downloading a dataset to test frangiPANe

frangiPANe test_install -d path_to_directory_that_contains_data

III - Run FrangiPANe

local mode

frangiPANe -e
frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2

cluster mode

::

module load python/3.8.12

frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml --cluster-config /scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml

#!/bin/bash

#SBATCH -J frangiPANe
#SBATCH -o frangiPANe."%j".out
#SBATCH -e frangiPANe."%j".err

#SBATCH --mail-user christine.tranchant@ird.fr
#SBATCH --mail-type=ALL

#SBATCH -p normal
#SBATCH -w node1
#SBATCH -c 1 # number of nodes

module load python/3.8.12
module load singularity/4.0.1
frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml

** example input**

IV - Outputs

tranchant@node1 tranchant]$ tree rice-output/
rice-output/
├── 01-fastq
│   ├── 01_mapped
│   │   ├── panref
│   │   └── ref
│   └── 02-filtered
│       └── ref
├── 02-assembly
│   ├── 01-abyss
│   ├── 02-filtered
│   ├── 03-vecscreen
│   └── 04-samples-merged
├── 03-clustering
│   ├── 01-cd-hit
│   └── 02-panreference
├── 04-stats
│   ├── 01-fastq
│   ├── 04-plots
│   └── 04-summary
├── LOGS
└── report

Authors

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

Reference

[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..