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These tutorials provide an easy introduction to the mapping algorithms implemented by various bioinformatics programs. In Section 2, we present a core set of algorithms necessary for understanding wide range of search programs. Section 3 discusses additional developments, which made the core tools run faster for large volume of data. In Section 4, we go under the hood for several popular mapping programs and describe their algoritms. Section 5 explores hardware-acceleration techniques utilized by a few mapping programs to speed up the executions. Section 6 covers references and future challenges.

We are thankful to Heng Li, whose insightful emails and comments helped us understand the most recent mapping algorithms. We also thank other readers of our blog for providing valuable insights.