"Milk Metagenomics Analysis of Cow Milk Samples across Global sites Using Mothur" was my Thesis title which I worked on, as a part of M. Tech in Biotechnology final year project. This study compares bacterial composition in cow and buffalo milk globally, considering environmental and host factors. Utilizing Mothur on Ubuntu environment, samples from diverse locations were analyzed. Results will elucidate the impact on milk microbiota and its correlation with quality, safety, and flavor. The study explores milk metagenomics for early detection of diseases like clinical mastitis, aiming to enhance dairy industry practices for improved milk quality and safety. ABOUT THE GIVEN PIPELINE The image shows the workflow of a RNA sequencing pipeline called "MOTHUR 16s RNA Pipeline." It starts with Data Pre-Processing, followed by Quality Control, Sequence Alignment, Pre-clustering, Taxonomic Classification, Distance Matrix Calculation, and OTUs analysis. The steps involve various tools and commands such as make.file, screen.seqs, chimera.search, align.seqs, unique.seqs, count.seqs, pre.cluster, classify.seqs, remove.lineage, dist.seqs, classify.otu, and cluster.seqs. The final outputs are Taxonomy Report, summary.tax, and Data Visualization in the form of Pivot Tables and Bar plots using MS-Excel.