ISMU 2.0: A Pipeline for Genomic Selection

Integrated SNPs mining and utilization (ISMU 1.0) pipeline was developed to analyze the next generation sequencing (NGS) data for variant analysis. ISMU 1.0 is a GUI based pipeline which offers a complete range of tools required for SNP analysis including data processing, alignment, mapping and variant detection. To utilize the genotyping information from the ISMU 1.0 together with available phenotypic information, ISMU 2.0 is being developed. Several data processing capabilities and genomic selection (GS) modules are being integrated in the existing pipeline. Several R and Fortran scripts including Ridge Regression Best Linear Unbiased Predictor (RR-BLUP), Kinship Gauss, Bayesian Ridge Regression, Bayesian LASSO, BayesA, BayesB, BayesCπ and Random Forest are being customized and integrated in to pipeline. Most of these scripts have been tested successfully on simulated datasets and now are in a process of being layered with a JAVA wrapper. Some scripts based on RR-BLUP integrated in GUI are being tested on real datasets from ICRISAT. Additionally, the pipeline has a module to check quality and different features of marker datasets such as % missing data, minor allele frequency (MAF) and polymorphism information content (PIC). The pipeline has been developed to run on 64-bit Linux. The pipeline is regularly tested on Windows, CentOS and Ubuntu platforms.