title: Analysis of next-generation sequencing data using Galaxy.
abstract: The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data. This chapter will focus on practical informatics methods, strategies, and software tools for transforming NGS data into usable information through the use of a web-based platform, Galaxy. The Galaxy interface is explored through several different types of example analyses. Instructions for running one's own Galaxy server on local hardware or on cloud computing resources are provided. Installing new tools into a personal Galaxy instance is also demonstrated.
authors.affiliation: Department of Biochemistry and Molecular Biology, Penn State University, 505 Wartik Laboratory, University Park, PA, 16802, USA, dan@bx.psu.edu.
authors.forename: Daniel
authors.initials: D
authors.lastname: Blankenberg
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hillman-Jackson
mesh_terms: D056808:Biostatistics / Q000379:methods*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface