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Brief Bioinform DOI:10.1093/bib/bbq015

A survey of sequence alignment algorithms for next-generation sequencing.

Publication TypeJournal Article
Year of Publication2010
AuthorsLi, H, Homer, N
JournalBrief Bioinform
Date Published2010 Sep
KeywordsAlgorithms, Base Sequence, Genome, Human, Humans, Sequence Alignment, Sequence Analysis, DNA, Software

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.


Alternate JournalBrief. Bioinformatics
PubMed ID20460430
PubMed Central IDPMC2943993
Grant List1U01HG005208-01 / HG / NHGRI NIH HHS / United States
1U01HG005210-01 / HG / NHGRI NIH HHS / United States