Assembly, Annotation and Visualization of NGS Data

The next-generation sequencing technologies have revolutionized the field of agriculture with the advent of ever-evolving chemistries and a reduction in the price of sequencing per base. The last decade has witnessed a substantial upsurge in the chemistries, databases, tools, and bioinformatics platforms. The number of data (GBs) deposited in publicly available databases is increasing exponentially day by day. From unraveling the basic structural information to understanding the minute patterns of gene functions, NGS technologies are being used to reveal various aspects of plant growth, development, stress resistance/tolerance, yield, nutrient content etc. on a modest budget. Climate change is also driving the need of more focused research using plant lines/germplasm for climate resilience. Availability of such data is extremely worthy in the current scenario of ever evolving chemistries, information technology, artificial intelligence. To have a conglomeration with the biological data, assembling, annotation and representation or visualization of the big data sets is extremely essential. These technologies include short read as well as long read sequencing individually or together offers high-throughput, scalability and speed by using various pipelines/platforms/graphical user interface. The tools and softwares deployed for executing the assembly, annotation and visualization need to be selected carefully based on the aims and applications of the study. The plausible roles of genetics and epigenetic regulation in a particular tissue and condition can be very well studied using different applications like genome sequencing, epigenetic, methylome sequencing, transcriptome sequencing, targeted sequencing etc. In this review, we have presented an account of the considerations for assembling the reads together, annotation, visualization for various applications along with various tools available for executing the same.