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Course Note on 'Algorithms for DNA sequencing'

Part1: Alignment

Chapter1: Exact matching

Algorithm that preprocesses T is offline, otherwise algorithm is online

• Online algorithms:
  • naive brute-force algorithm && Boyer-Moore algorithm
• Index-assisted offline algorithms:
  • k-mer index
  • subseq index
    • Suffix Tree
    • FM index

Chapter2: Approximate matching

• Preface
• Approaches to carry out approximate matching
• the clever combinations of ideas: index + dynamic programming

Part2: Assembly

Assembly theory

Assembly algorithms

Assembly in practice

Long reads and assembly