A survey of sequence alignment algorithms for next-generation sequencing

Briefings in Bioinformatics

Volumn 11, Issue 5, 2010, Pages 473-483

  Li, Heng ^a   Homer, Nils ^b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alignment algorithm; New sequencing technologies; Sequence analysis

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; DNA SEQUENCE; HUMAN; HUMAN GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE; REVIEW; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; GENOME, HUMAN; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 77957272611     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbq015     Document Type: Review

References (71)

1. Dalca AV, Brudno M. Genome variation discovery with high-throughput sequencing data. Brief Bioinform 2010;11: 3-14.
2. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009;6:S22-32.
3. Cokus SJ, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008;452:215-9.
4. Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods 2009;6:S6-12.
5. Simpson JT, Wong K, Jackman SD, et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009;19: 1117-23.
6. Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265-72.
7. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010;11:31-46.
8. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001;11:1725-9.
9. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002;12:656-64.
10. Malhis N, Butterfield YSN, Ester M, et al. Slider-maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics 2009;25: 6-13.
11. Malhis N, Jones SJ. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics 2010;26:1029-35.
12. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
13. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
14. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-7.
15. Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol 1982;162:705-8.
16. Ma B, Tromp J, Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 2002;18:440-5.
17. Li R, Li Y, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713-4.
18. Jiang H, Wong WH. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008;24: 2395-6.
19. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008;18:1851-8.
20. Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 2008;9:128.
21. Smith AD, Chung WY, Hodges E, et al. Updates to the RMAP short-read mapping software. Bioinformatics 2009;25: 2841-2.
22. Baeza-Yates RA, Perleberg CH. Fast and practical approx-imate string matching. In: Apostolico A, Crochemore M, Galil Z, Manber U, (eds). CPM, Lecture Notes in Computer Science, Vo l. 6 4 4. Berlin: Springer, 1992:185-92.
23. Lin H, Zhang Z, Zhang MQ, et al. ZOOM! Zillions of oligos mapped. Bioinformatics 2008;24:2431-7.
24. Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010; 26:873-81.
25. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoSOne 2009;4: e7767.
26. Schatz M. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009;25:1363-9.
27. Chen Y, Souaiaia T, Chen T. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 2009;25:2514-21.
28. Clement NL, Snell Q, Clement MJ, et al. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleo-tides from next-generation sequencing. Bioinformatics 2010; 26:38-45.
29. Rumble SM, Lacroute P, Dalca AV, et al. SHRiMP: accu-rate mapping of short color-space reads. PLoS Comput Biol 2009;5:e1000386.
30. Weese D, Emde AK, Rausch T, et al. RazerS-fast read mapping with sensitivity control. Genome Res 2009;19: 1646-54.
31. Jokinen P, Ukkonen E. Two algorithms for approximate string matching in static texts. In: MFCS, Lecture Notes in Computer Science, Vo l. 5 2 0. Berlin: Springer, 1991:240-8.
32. Cao X, Li SC, Tung AKH. Indexing DNA sequences using q-Grams. In: Zhou L, Ooi BC, Meng X, (eds). DASFAA, Lecture Notes in Computer Science, Vol. 3453. Berlin: Springer, 2005:4-16.
33. Burkhardt S, Kärkkäinen J. Better filtering with gapped q-grams. In: Apostolico A, Takeda M, (eds). CPM, Lecture NotesinComputerScience, Vo l. 2 0 8 9. Berlin: Springer, 2001:73-85.
34. Farrar M. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 2007;23:156-61.
35. Eppstein D, Galil Z, Giancarlo R, Italiano GF. Sparse dynamic programming. In: SODA. Philadelphia: Society for Industrial and Applied Mathematics, 1990;513-22.
36. Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005;6:31.
37. Myers EW. An O(ND) Difference algorithm and its variations. Algorithmica 1986;1(2):251-66.
38. Abouelhoda MI, Kurtz S, Ohlebusch E. Replacing suffix trees with enhanced suffix arrays. JDiscreteAlgorithms2004;2: 53-86.
39. Ferragina P, Manzini G. Opportunistic data structures with applications. In: Proceedings of the 41st Symposium on Foundations of Computer Science (FOCS 2000), Redondo Beach, CA, USA. 2000;390-8.
40. Burrows M, Wheeler DJ. A block-sorting lossless data com-pression algorithm. Technical Report 124, Digital Equipment Corporation. CA: Palo Alto, 1994.
41. Munro JI, Raman V, Rao SS. Space efficient suffix trees. J Algorithms 2001;39(2):205-22.
42. Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biol 2004;5: R12.
43. Manber U, Myers EW. Suffix arrays: a new method for on-line string searches. SIAM J Comput 1993;22: 935-48.
44. Navarro G. A guided tour to approximate string matching. ACM Comput Surv 2001;33:31-88.
45. Meek C, Patel JM, Kasetty S. OASIS: an online and accu-rate technique for local-alignment searches on biological sequences. In: Proceedings of 29th International Conference on Very Large Data Bases (VLDB 2003), Berlin. 2003;910-21.
46. Hoffmann S, Otto C, Kurtz S, et al. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 2009;5:e1000502.
47. Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25.
48. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25: 1754-60.
49. Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009; 25:1966-7.
50. Lam TW, Sung WK, Tam SL, et al. Compressed index-ing and local alignment of DNA. Bioinformatics 2008;24: 791-7.
51. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26(5):589-95.
52. Blumer A, Blumer J, Haussler D, et al. The smallest auto-maton recognizing the subwords of a text. Theoretical Computer Science 1985;40:31-55.
53. Ossowski S, Schneeberger K, Clark RM, et al. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 2008;18:2024-2033.
54. Krawitz P, Rödelsperger C, Jäger M, et al. Microindel detection in short-read sequence data. Bioinformatics 2010; 26:722-9.
55. Chen K, Wallis JW, McLellan MD, et al. BreakDancer: an algorithm for high-resolution mapping of genomic struc-tural variation. Nat Methods 2009;6:677-81.
56. Homer N, Merriman B, Nelson SF. Local alignment of two-base encoded DNA sequence. BMC Bioinformatics 2009;10:175.
57. Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009;10:232.
58. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8.
59. De Bona F, Ossowski S, Schneeberger K, et al. Optimal spliced alignments of short sequence reads. Bioinformatics 2008;24:i174-80.
60. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-11.
61. Anson EL, Myers EW. ReAligner: a program for refining DNA sequence multi-alignments. J Comput Biol 1997;4(3): 369-83.
62. Li H, Handsaker B, Wysoker A, et al. The sequence align-ment/map format and SAMtools. Bioinformatics 2009;25: 2078-9.
63. Stein LD, Mungall C, Shu S, et al. The generic genome browser: a building block for a model organism system database. Genome Res 2002;12(10):1599-610.
64. Manske HM, Kwiatkowski DP. LookSeq: a browser-based viewer for deep sequencing data. Genome Res 2009;19(11): 2125-32.
65. Milne I, Bayer M, Cardle L, et al. Tablet-next generation sequence assembly visualization. Bioinformatics 2010;26(3): 401-2.
66. Carver T, Bohme U, Otto T, et al. BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 2010;26(5):676-7.
67. Koboldt DC, Chen K, Wylie T, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009;25:2283-5.
68. Langmead B, Schatz MC, Lin J, et al. Searching for SNPs with cloud computing. Genome Biol 2009;10(11):R134.
69. Li R, Li Y, Zheng H, et al. Building the sequence map of the human pan-genome. Nat Biotechnol 2010;28:57-63.
70. Schneeberger K, Hagmann J, Ossowski S, et al. Simultaneous alignment of short reads against multiple genomes. Genome Biol 2009;10:R98.
71. Mäkinen V, Navarro G, Sirén J, et al. Storage and retrieval of individual genomes. In: Batzoglou S (ed). RECOMB, Lecture Notes in Computer Science,Vol. 5541. Berlin: Springer, 2009;121-37.