Bioinformatics tools and databases for analysis of next-generation sequence data

Briefings in Functional Genomics

Volumn 11, Issue 1, 2012, Pages 12-24

  Lee, Hong C ^a   Lai, Kaitao ^a   Lorenc, Michał Tadeusz ^a   Imelfort, Michael ^a   Duran, Chris ^a   Edwards, David ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

De novo sequencing; Next generation sequencing; Second generation sequencing; Sequence alignment; Sequence assembly; Short reads; Visualization

Indexed keywords

GENOMIC DNA;

ARTICLE; ASSEMBLY BY SHORT SEQUENCE; BIOINFORMATICS; BLAT LIKE FAST ACCURATE SEARCH TOOL; DATA ANALYSIS SOFTWARE; DATA STORAGE DEVICE; DE NOVO GENOME ASSEMBLY; DNA SEQUENCE; GENE DOSAGE; GENE MAPPING; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC MARKER; HUMAN; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PAIRED END ASSEMBLER; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SHORT OLIGONUCLEOTIDE ANALYSIS PACKAGE; SHORT READ ASSEMBLY; SHORT READ MAPPING PACKAGE; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE; STATISTICS AS TOPIC; TRANSCRIPTOME;

EID: 84863126127     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elr037     Document Type: Article

References (76)

1. Edwards D, Batley J. Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 2010;7:1-8.
2. Imelfort M, Edwards D. De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 2009;10:609-18.
3. Imelfort M, Batley J, Grimmond S, et al. Genome sequencing approaches and successes. In: Somers D, Langridge P, Gustafson J (eds). Plant Genomics. USA: Humana Press, 2009:345-58.
4. Lin Y, Li J, Shen H, et al. Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 2011;27:2031-7.
5. Zhang W, Chen J, Yang Y, et al. A practical comparison of de novo genome assembly software tools for nextgeneration sequencing technologies. Plos One 2011;6: e17915.
6. Warren RL, Sutton GG, Jones SJM, et al. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 2007;23:500-1.
7. Jeck WR, Reinhardt JA, Baltrus DA, et al. Extending assembly of short DNA sequences to handle error. Bioinformatics 2007;23:2942-4.
8. Dohm JC, Lottaz C, Borodina T, et al. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 2007;17:1697-706.
9. Hernandez D, Francois P, Farinelli L, et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 2008;18:802-9.
10. Butler J, MacCallum I, Kleber M, et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008;18:810-20.
11. MacCallum I, Przybylski D, Gnerre S, et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 2009;10: R103.
12. Gnerre S, MacCallum I, Przybylski D, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 2011;108: 1513-8.
13. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-9.
14. Zerbino DR, McEwen GK, Margulies EH, et al. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. Plos One 2009;4(12):e8407.
15. Simpson JT, Wong K, Jackman SD, et al. ABySS: a parallel assembler for short read sequence data. GenomeRes 2009;19: 1117-23.
16. Pevzner PA, Tang HX, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001;98:9748-53.
17. Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. GenomeRes 2008;18:324-30.
18. Li RQ, Li YR, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24: 713-4.
19. Li RQ, Zhu HM, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265-72.
20. Li RQ, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010; 463:1106.
21. Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature 2008;456:60-5.
22. The Brassica rapa Genome Sequencing Project Consortium. The genome of the mesopolyploid crop species Brassica rapa. Nature Genet 2011;43:1035-40.
23. Berkman BJ, Skarshewski A, Lorenc MT, et al. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 2011;9:768-75.
24. Myers EW. Toward simplifying and accurately formulating fragment assembly. JComputBiol 1995;2:275-90.
25. Ariyaratne PN, Sung W-K. PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 2011; 27:167-74.
26. Kent W. BLAT - the BLAST-like alignment tool. Genome Res 2002;12:656-64.
27. Karolchik D, Kuhn RM, Baertsch R, et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008;36:D773-9.
28. Flicek P, Amode MR, Barrell D, et al. Ensembl 2011. Nucleic Acids Res 2011;39:D800-6.
29. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008;18:1851-8.
30. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. Plos One 2009;4: e7767.
31. 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.
32. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-9.
33. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-11.
34. Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010;28:511-5.
35. Li R, Li Y, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713-4.
36. Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009;25:1966-7.
37. Horner DS, Pavesi G, Castrignano T, et al. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinformatics 2010;11: 181-97.
38. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25: 1754-60.
39. Rumble S, Lacroute P, Dalca A, et al. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 2009; 5:1000386e.
40. David M, Dzamba M, Lister D, et al. SHRiMP2: sensitive yet practical short read mapping. Bioinformatics 2011;27: 1011-2.
41. Marshall D, Hayward A, Eales D, et al. Targeted identification of genomic regions using TAGdb. Plant Methods 2010; 6:19.
42. Zhang Z, Schwartz S, Wagner L, et al. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000;7: 203-14.
43. Duran C, Appleby N, Edwards D, et al. Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 2009;4:16-27.
44. Quinlan AR, Stewart DA, Stromberg MP, et al. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 2008;5:179-81.
45. Marth GT, Korf I, Yandell MD, et al. A general approach to single-nucleotide polymorphism discovery. Nat Genetics 1999;23:452-6.
46. Novaes E, Drost DR, Farmerie WG, et al. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008;9:312.
47. Barbazuk WB, Emrich SJ, Chen HD, et al. SNP discovery via 454 transcriptome sequencing. Plant Journal 2007;51: 910-18.
48. Brockman W, Alvarez P, Young S, et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008;18:763-70.
49. Barker G, Batley J, O'Sullivan H, et al. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 2003;19:421-2.
50. Batley J, Barker G, O'Sullivan H, et al. Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 2003;132:84-91.
51. Duran C, Appleby N, Clark T, et al. AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 2009;37:D951-3.
52. Duran C, Appleby N, Vardy M, et al. Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant BiotechnolJ 2009;7:326-33.
53. Imelfort M, Duran C, Batley J, et al. Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J 2009;7:312-7.
54. Lai JS, Li RQ, Xu X, et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 2010;42: 1027-158.
55. Huang XH, Wei XH, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 2010;42:961-76.
56. Duran C, Eales D, Marshall D, et al. Future tools for association mapping in crop plants. Genome 2010;53: 1017-23.
57. Edwards KJ, Barker JHA, Daly A, et al. Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 1996;20:758.
58. Robinson AJ, Love CG, Batley J, et al. Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 2004;20:1475-6.
59. Jewell E, Robinson A, Savage D, et al. SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Res 2006;34:W656-9.
60. Santana QC, Coetzee MPA, Steenkamp ET, et al. Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 2009;46:217-23.
61. Abdelkrim J, Robertson BC, Staton JL, et al. Fast, costeffective development of species specific microsatellite markers by genomic sequencing. Biotechniques 2009;46: 185-192.
62. Jennings TN, Knaus BJ, Mullins TD, et al. Multiplexed microsatellite recovery using massively parallel sequencing. Mol Ecol Resour 2011;11(6):1060-67.
63. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-11.
64. 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.
65. Doering A, Weese D, Rausch T, et al. SeqAn An efficient, generic C++ library for sequence analysis. BMC Bioinformatics 2008;9:11.
66. Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech 2010;28:511-5.
67. Edmonson MN, Zhang J, Yan C, et al. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics 2011;27: 865-6.
68. Gordon D, Abajian C, Phil G. Consed: a graphical tool for sequence finishing. Genome Res 1998;8:195-202.
69. Milne I, Bayer M, Cardle L, et al. Tablet-next generation sequence assembly visualization. Bioinformatics 2010;26: 401-2.
70. Robinson JT, Thorvaldsdottir H, Winckler W, et al. Integrative genomics viewer. Nat Biotech 2011;29:24-6.
71. Fiume M, Williams V, Brook A, et al. Savant: genome browser for high-throughput sequencing data. Bioinformatics 2010;26:1938-44.
72. Hou H, Zhao F, Zhou L, et al. MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. Nucleic Acids Res 2010;38:W732-6.
73. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20:1297-303.
74. Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011;27: 2156-8.
75. Drummond AJ, Ashton B, Buxton S, et al. Geneious v5.4. http://www.geneious.com/.
76. Batley J, Edwards D. Genome sequence data: management, storage, and visualization. Biotechniques 2009;46: 333-6.