Emerging Tools for Generating Genomics Data

Genomics is one of the multi-omics branches which deals with the study of the complete genomes of organisms. It probes into the structure, function, and inheritance of an organism’s genome, by determining the sequence of their genomic DNA or RNA. Genomics can hence be categorized based on their study outputs such as Functional genomics which deals with the gene and protein functions, Structural genomics which focuses on determining and analyzing the three-dimensional structures of biological macromolecules, Epigenomics which delves into the chemical modifications of DNA and their role in gene expression, and Metagenomics which involves analyzing genomes within environmental samples. The genome analysis encompasses an array of molecular methods involving a wide combination of recombinant DNA (by cloning into vectors), sequencing techniques, and bioinformatics algorithms to generate accurate genomic data. The advancements in molecular biology and bioinformatics have revolutionized genome analysis, leading to the development of various methods catering to different levels of genomic study. High-throughput sequencing technologies have facilitated large-scale genome analysis while advancements in the bioinformatics forefront have accurately yielded comprehensive data sets. This chapter provides an overview of methods for generating genomic data by categorizing the techniques based on a) Throughputs such as high-throughput and low-throughput sequencing methods which involve versions of NGS and Sanger-seq, respectively, b) Principles of sequencing strategies like shotgun sequencing, targeted sequencing, epigenome and chromosomal level analysis, and short tandem repeat (STR) analysis, along with their applications and c) Molecular cloning which enables gene mapping and functional genomic studies. Furthermore, the chapter addresses computational tools and bioinformatics pipelines crucial for genome assembly, alignment, variant calling, and functional annotation, emphasizing their vital role in decoding genomic data.