Montasio Natural Milk Culture

Code for the paper "Integrated approach to explore the microbial biodiversity of natural milk culture for Montasio cheese production", published in Journal of Dairy Science (https://doi.org/10.3168/jds.2024-24463). If you find the code useful, please cite the publication!

Required software

• R (we used R 3.6.1, any newer version should do)
• kraken2 (we used 2.1.2)

Used data

• Reads can be retrieved from SRA, under accession PRJNA916949
• Physicochemical parameter data can be found in the 06_chempar folder of this repository

Instructions

• Create a folder for the project e.g. myhome/lattoinnesto and store it in the variable BASEDIR, i.e. BASEDIR=myhome/lattoinnesto
• Download the reads from SRA accession PRJNA916949 and store them in the project folder, in a subfolder called "01_raw_reads"
• Download the repository in the project folder
• Create the folder ${BASEDIR}/databases and download the kraken DB in the folder. Please find instructions on installing kraken2 databases here. Note: one of the DB I used (minikraken2_v2_8GB_201904_UPDATE) is relatively old. You may want to use a newer one, and you will need to change the folder ${BASEDIR}/databases/minikraken2_v2_8GB_201904_UPDATE to ${BASEDIR}/databases/newDBname.
• Edit the lines in the 00_lattoinnesto_workflow.sh file where local variables are stored. Remember to uncomment the variables.
• Run the 00_lattoinnesto_workflow.sh file. I suggest you execute the commands step by step by copying and pasting them in the terminal, so that you can spot mistakes immediately. There may be errors due to wrong folder structure (my fault!), or due to missing software (not my fault!)