This repository allow the analysis of data obtained from the Illumina sequencing of ITS region of fungi in an enviromental sample. Qiime2 need a linux enviroment to work.

1. download WSL for windows and Ubuntu distro.
2. install conda for linux
3. clone the repo git clone git clone https://github.com/ChiaraMorena/MetabarcodingCornSeeds
4. create an enviroment with the .yml file of the repo conda env create -f MetabarcodingCornSeeds/snakemake-qiime2.yml and activate conda activate snakemake
5. connect positron or vsc to the WLS: sudo apt-get install openssh-server sudo service ssh start trova ip con : ip a vai in positron clicca sui due >< in basso a sx e connetti host inserisci il nome_utente_linux@ip e la password open folder -> cartella con la repo start session : scegli il tuo enviroment