Beef_calf_rumen

This repository contains the code for bioinformatic and R analysis of the paper "Effect of castration timing and weaning strategy on the rumen metagenome of beef calves"

General information

1. Project: MBC Project - MS Thesis Gerardo R Diaz (Chapter 01) - College of Veterinary Medicine, University of Minnesota
2. Samples: Ruminal fluid
3. Sequencing method: Shotgun metagenomics
4. Date: 2021 - 2023
5. Author: Gerardo R. Diaz ([email protected])
6. Description: This dry lab bitacora contains the code and processes followed during the bionformatic analysis of the MBC project which was also the chapter 01 of MS thesis of Gerardo R Diaz (EFFECT OF EARLY-LIFE MANAGEMENT PRACTICES ON THE RUMEN METAGENOME OF BEEF CATTLE).

Contains:

1. Microbiome and AMR genes analysis (AMRplusplus)
2. R_microbiome_rumen
3. R_AMR_rumen
4. Methanogens analysis (MCycDB)
5. R_methanogens_rumen
6. MAG building (Megahit, metawrap, dRep, GTDBTk)
7. R_MAG_poster
8. Others (Extra process like Metaphlan, Humman3, etc)

WARNING:

Check software versions, paths and dependencies because they may have changed. Keep in mind that this code was adapted to my particular needs. Welcome!