NexGen sequencing data: Bioinformatic tools for visualization and analysis

Since the onset of DNA sequencing, the need for sequence analysis and visualization has emerged and quickly become a central aspect of research. From the early days in the 1970's and 80's until the late 1990's a predominant focus was put on visualizing individual genes and regulatory elements such as promoters and terminator structures, where one of the biggest entities investigated were bacteriophages comprising 40 to 200 genes. Similarly, comparative analyses were mostly limited to genes, operons or plasmids with often manual interrogation and visualization of the sequence data. With the advent of next generation sequencing platforms in the early 2000's, the volume of available DNA sequence data is growing exponentially. Draft and complete bacterial genomes have emerged, necessitating new ways of automatically analyzing, comparing and visualizing thousands of genes in their respective contexts. Metagenomics and multi-omic data integration, combining layers of omic technologies, represent the next challenge for meaningful data interrogation. Consequently, many different conceptual approaches and tools have been developed to address the varying needs of DNA sequence assembly, genome annotation, comparative analyses and their visual representations. In this book chapter, current trends and tools employed in genomic sciences are introduced. The sheer number of approaches makes it impossible to introduce every possible system available; instead, the chapter focuses on representative examples that introduce different fundamental concepts of sequence analyses and visualisations, guiding through important considerations when deciding on and carrying out genomic analyses.