title: A survey of sequence alignment algorithms for next-generation sequencing.
abstract: 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.
authors.affiliation: Broad Institute, Cambridge, MA 02142, USA. hengli@broadinstitute.org
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Nils
authors.initials: N
authors.lastname: Homer
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015894:Genome, Human; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
references.citation: Genome Res. 2001 Oct;11(10):1725-9
references.pmid: 11591649
references.citation: BMC Bioinformatics. 2009 Jun 09;10:175
references.pmid: 19508732
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Bioinformatics. 2009 Jun 1;25(11):1363-9
references.pmid: 19357099
references.citation: PLoS Comput Biol. 2009 May;5(5):e1000386
references.pmid: 19461883
references.citation: Genome Res. 2008 Dec;18(12):2024-33
references.pmid: 18818371
references.citation: Bioinformatics. 2010 Mar 1;26(5):676-7
references.pmid: 20071372
references.citation: Bioinformatics. 2010 Apr 1;26(7):873-81
references.pmid: 20147302
references.citation: Bioinformatics. 2010 Apr 15;26(8):1029-35
references.pmid: 20190250
references.citation: Bioinformatics. 2010 Mar 15;26(6):722-9
references.pmid: 20144947
references.citation: Brief Bioinform. 2010 Jan;11(1):3-14
references.pmid: 20053733
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: PLoS Comput Biol. 2009 Sep;5(9):e1000502
references.pmid: 19750212
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Bioinformatics. 2009 Oct 1;25(19):2514-21
references.pmid: 19675096
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Genome Biol. 2009;10(11):R134
references.pmid: 19930550
references.citation: Genome Res. 2009 Nov;19(11):2125-32
references.pmid: 19679872
references.citation: BMC Bioinformatics. 2009 Jul 27;10:232
references.pmid: 19635165
references.citation: Genome Biol. 2009;10(9):R98
references.pmid: 19761611
references.citation: Nat Methods. 2009 Sep;6(9):677-81
references.pmid: 19668202
references.citation: Genome Res. 2009 Sep;19(9):1646-54
references.pmid: 19592482
references.citation: Bioinformatics. 2009 Jan 1;25(1):6-13
references.pmid: 18974170
references.citation: Bioinformatics. 2010 Mar 1;26(5):589-95
references.pmid: 20080505
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: BMC Bioinformatics. 2005 Feb 15;6:31
references.pmid: 15713233
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: BMC Bioinformatics. 2008 Feb 28;9:128
references.pmid: 18307793
references.citation: Bioinformatics. 2002 Mar;18(3):440-5
references.pmid: 11934743
references.citation: J Comput Biol. 1997 Fall;4(3):369-83
references.pmid: 9278066
references.citation: PLoS One. 2009 Nov 11;4(11):e7767
references.pmid: 19907642
references.citation: Nat Biotechnol. 2010 Jan;28(1):57-63
references.pmid: 19997067
references.citation: Bioinformatics. 2008 Mar 1;24(5):713-4
references.pmid: 18227114
references.citation: Bioinformatics. 2008 Oct 15;24(20):2395-6
references.pmid: 18697769
references.citation: Bioinformatics. 2010 Jan 1;26(1):38-45
references.pmid: 19861355
references.citation: Bioinformatics. 2010 Feb 1;26(3):401-2
references.pmid: 19965881
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S6-S12
references.pmid: 19844229
references.citation: Nature. 2008 Mar 13;452(7184):215-9
references.pmid: 18278030
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Genome Res. 2008 Nov;18(11):1851-8
references.pmid: 18714091
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S22-32
references.pmid: 19844228
references.citation: Bioinformatics. 2008 Mar 15;24(6):791-7
references.pmid: 18227115
references.citation: J Mol Biol. 1982 Dec 15;162(3):705-8
references.pmid: 7166760
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: J Mol Biol. 1981 Mar 25;147(1):195-7
references.pmid: 7265238
references.citation: Bioinformatics. 2009 Sep 1;25(17):2283-5
references.pmid: 19542151
references.citation: Bioinformatics. 2007 Jan 15;23(2):156-61
references.pmid: 17110365
references.citation: Bioinformatics. 2008 Aug 15;24(16):i174-80
references.pmid: 18689821
references.citation: Bioinformatics. 2008 Nov 1;24(21):2431-7
references.pmid: 18684737
references.citation: Bioinformatics. 2009 Nov 1;25(21):2841-2
references.pmid: 19736251
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Genome Res. 2002 Oct;12(10):1599-610
references.pmid: 12368253