This lecture was part of the lecture delivered by Dr. Kibret at Plant Breeding Academy at UCDavis, VIII Week 3 _ Seed Biotechnology Center. Breeding and agronomy researchers and companies need to use a myriad of tools working in different operating systems, e.g. Some work only on Linux. From field trial and nursery design to genomic data analysis, there are hundreds of steps and software. Moreover, these tasks involve big data analysis. The aim of this lecture was to provide solutions for reliable open-source analysis pipeline that provides the much-needed functionalities and the gap in current breeding and molecular biology computational tools. The lecture covers the most in-demand topics much needed among breeders and graduate students working on a breeding project. The topics include: i) get a list of informative/polymorphic SNPs and their primers for the crop of interest, ii) Access the reference genome, iii) SNPs discovery and filtering iv) once the data is back to the company from the service provider for genotyping, where they can store the row data v) run PCA for in routine or GWAS, genomic prediction etc vi) run GWAS, genomic prediction and other genomic algorithms vii) run transcriptome data analysis