Abstract

This chapter discusses how to connect from one's desktop to their Amazon Web Services data and visualize and analyze remote Binary Alignment Map files. Genome visualizer is a graphical tool that allows one to visualize genomic data. The sequence of a genome is usually displayed as a horizontal line. Integrative Genomics Viewer (IGV) is a very comprehensive and customizable genome browser. It can handle a large variety of file formats and offers a lot of functionalities, while remaining easy to use. For these reasons, IGV is a popular genome visualizer. The chapter focuses on the desktop version of IGV. The IGV browser can visualize remote files without downloading the whole file. IGV supports two formats for genome references: the traditional FASTA format and an IGV proprietary format called .genome. CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. It is a compressed representation of an alignment that is part of the SAM file format.

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