Genome-Scale Algorithm Design

Presenting the fundamental algorithms and data structures that power bioinformatics workflows this book covers a range of topics from the foundations of sequence analysis (alignments and hidden Markov models) to classical index structures (k-mer indexes suffix arrays and suffix trees) Burrows-Wheeler indexes graph algorithms network flows and a number of advanced omics applications. The chapters feature numerous examples algorithm visualizations and exercises providing graduate students researchers and practitioners with a powerful algorithmic toolkit for the applications of high-throughput sequencing. An accompanying website (www.genome-scale.info) offers supporting teaching material. The second edition strengthens the toolkit by covering minimizers and other advanced data structures and their use in emerging pangenomics approaches.