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Table 2 Advantages and limitations of read alignment algorithms. We compare the ease of implementing each algorithm (“Easy to implement”). We define the “ease of implementation” as the ability to quickly implement such an algorithm and its indexing technique, flexibly apply some changes to it, and easily understand its working principle. We also record whether the algorithm allows for an exact and/or inexact match (“Search for exact/inexact match”). The use of spaced seeds enables searching for inexact match using a hash table. We also compare the size of the genome index (indicated in column “Index size”), the speed of seed query (indicated in column “Seed query speed”), and the possibility to vary the length of the seed (“Seed length”)

From: Technology dictates algorithms: recent developments in read alignment

  Hashing Suffix tree and BWT-FM
Easy to implement Yes No
Search for exact/inexact match Exact Exact and inexact
Index size Large Compressed (small)
Indexing time Small Large
Seed query speed O(1), fast Slow
Seed length Fixed length per index Can be fixed or variable