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The development of "next-generation" high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago. Although the scientifi c applications are diverse, e.g., new genome projects, gene expression analysis, genome-wide functional screens, or epigenetics-the sequence data are usually processed in one of two ways: sequence reads are either mapped to an existing reference sequence, or they aredoi:10.1007/978-1-4939-1438-8_2 pmid:25388106 fatcat:dobmztvzlbctbf6yjz24cshake