INRB-LaBiEp-DENGUE

This folder contains codes to analyse dengue reads from nanopore platfrom for the outbreak in CHAD

The Pipeline is named DENVAP : Dengue Virus Analysis Pipeline

Installation of DENVAP

The installation is very simple but requires some requisites

1. Conda:

Linux

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o ~/Miniconda3-latest-Linux-x86_64.sh && \
bash ~/Miniconda3-latest-Linux-x86_64.sh  && \
rm -f ~/Miniconda3-latest-Linux-x86_64.sh

MacOS

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/Miniconda3-latest-MacOSX-x86_64.sh && \
bash ~/Miniconda3-latest-MacOSX-x86_64.sh && \
rm -f ~/Miniconda3-latest-MacOSX-x86_64.sh

2. Mamba:

conda install -c conda-forge mamba

3. DENVAP:

git clone --recursive https://github.com/inrb-labgenpath/INRB-LaBiEp-DENGUE.git

cd INRB-LaBiEp-DENGUE
chmod u+x {*yaml,*sh,*smk,*.py}
mamba env create -f DENVAP.yaml

Usage

1. Load the reads

Load your reads in the fastq folder, make sure your barcode name length is 24 characters
barcode01 ---> XXXXXXXXXXXXXX_barcode01
e.g: barcode01 ---> 23-COG-DENV001_barcode01
Hopefully you may use whatever length you want the next version of the pipeline

2. Run the script

conda activate denvap

bash --verbose DENVAP.sh

3. Reset the folder *Make sure you save in another folder all the analysis, go to the INRB-LaBiEp-DENGUE location

rm -rf ./*
git reset --hard e33ce9964b78710560c2f3bdfee7818f11312cd0