A number of publicly available stand-alone genome browser tools [114], including Artemis [115], EagleView [116], MapView [117], Tablet [118], Savant [119], and Apollo [120], can be used to visualize raw tag density profiles (and enriched genomic regions, see below) in relation to available annotation tracks. The University of California Santa Cruz (UCSC) [121] and the Integrative Genomics Viewer (IGV) [122] represent some of the most powerful options currently. UCSC provides a plethora of information on whole-genome and exome sequencing, epigenetic and expression data, single nucleotide polymorphisms (SNPs), repeat elements and functional information from the ENCODE and other research projects. It supports incorporation of personally generated data as BED, BedGraph, GFF, WIG and BAM files, so that a researcher can compare his/her own data directly with the publicly available one. IGV represents another efficient, high-performance and intuitive genomics visualization and exploration tool, characterized by its ability to handle large and diverse datasets on a desktop computer. The user can input a variety of data types to compare them with publicly available data from the ENCODE, Cancer Genome Atlas [123], 1000 Genomes [124] and other projects.
