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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.
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