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1.  A survey of sequence alignment algorithms for next-generation sequencing 
Briefings in Bioinformatics  2010;11(5):473-483.
Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing.
doi:10.1093/bib/bbq015
PMCID: PMC2943993  PMID: 20460430
new sequencing technologies; alignment algorithm; sequence analysis

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