A survey of sequence alignment algorithms for next-generation sequencing

Heng Li and Nils Homer, A survey of sequence alignment algorithms for next-generation sequencing, Briefings in Bioinformatics 2(5), 2010

Depending on the property of the index, alignment algorithms can be largely grouped into three categories; algorithms based on hash tables, algorithms based on suffix trees and algorithms based on merge sorting.

The development of alignment algorithms has been successful and short-read alignment against a single reference is not the bottleneck in data analyses any more.

With the increasing read lengths produced by the new sequencing technologies, we except further development in multi-reference alignment, long-read alignment and de novo assembly.

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