Unraveling genomic variation from next generation sequencing data

BioData Mining

Volumn 6, Issue 1, 2013, Pages

  Pavlopoulos, Georgios A ^a   Oulas, Anastasis ^b   Iacucci, Ernesto ^c   Sifrim, Alejandro ^d   Moreau, Yves ^d   Schneider, Reinhard ^e   Aerts, Jan ^d   Iliopoulos, Ioannis ^a  

^a UNIVERSITY OF CRETE   (Greece)

^b Institute of Marine Biology   (Greece)

^c GHENT UNIVERSITY   (Belgium)

^d UNIVERSITY OF LEUVEN   (Belgium)

^e UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

CNV; Genome browser; Genome wide association studies; Polymorphisms; Sequencing; SNPs; SNVs; Structural variation; Visualization

Indexed keywords

CONTIG; DNA FRAGMENT; RESTRICTION ENDONUCLEASE; RNA;

BIOINFORMATICS; CHROMOSOME TRANSLOCATION; COPY NUMBER VARIATION; DNA LIBRARY; DNA SEQUENCE; EPIGENETICS; EXOME; GEL ELECTROPHORESIS; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOMICS; HAPLOTYPE MAP; HUMAN; HUMAN GENOME; NEXT GENERATION SEQUENCING; NONHUMAN; PERSONALIZED MEDICINE; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84880858660     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/1756-0381-6-13     Document Type: Review

References (125)

1. Finishing the euchromatic sequence of the human genome. Nature 2004 431 7011 931 945 PMID: 15496913 10.1038/nature03001 15496913 (Pubitemid 39434409)
2. Initial sequencing and analysis of the human genome. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Nature 2001 409 6822 860 921 10.1038/35057062 11237011 (Pubitemid 32165345)
3. The diploid genome sequence of an individual human. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al. PLoS Biol 2007 5 10 254 10.1371/journal.pbio.0050254 17803354 (Pubitemid 350035416)
4. A map of human genome variation from population-scale sequencing. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, Nature 2010 467 7319 1061 1073 10.1038/nature09534 20981092
5. An integrated map of genetic variation from 1,092 human genomes. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, Nature 2012 491 7422 56 65 10.1038/nature11632 23128226
6. A comparison of cataloged variation between international HapMap consortium and 1000 genomes project data. Buchanan CC, Torstenson ES, Bush WS, Ritchie MD, J Am Med Inform Assoc 2012 19 2 289 294 10.1136/amiajnl-2011-000652 22319179
7. [International HapMap project]. Tanaka T, Nihon Rinsho 2005 12 63 Suppl 29 34
8. The international HapMap project Web site. Thorisson GA, Smith AV, Krishnan L, Stein LD, Genome Res 2005 15 11 1592 1593 10.1101/gr.4413105 16251469 (Pubitemid 41545013)
9. Integrating ethics and science in the international HapMap project. Nat Rev Genet 2004 5 6 467 475 PMID: 15153999 10.1038/nrg1351 15153999 (Pubitemid 38915413)
10. The international HapMap project. Nature 2003 426 6968 789 796 PMID: 14685227 10.1038/nature02168 14685227 (Pubitemid 38056856)
11. Estimating the size of the world's threatened flora. Pitman NC, Jorgensen PM, Science 2002 298 5595 989 10.1126/science.298.5595.989 12411696 (Pubitemid 35247299)
12. The 1001 genomes project for arabidopsis thaliana. Weigel D, Mott R, Genome Biol 2009 10 5 107 10.1186/gb-2009-10-5-107 19519932
13. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered 2009 100 6 659 674 PMID: 19892720 19892720
14. The microbial pan-genome. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R, Curr Opin Genet Dev 2005 15 6 589 594 10.1016/j.gde.2005.09.006 16185861 (Pubitemid 41532330)
15. The next generation: using new sequencing technologies to analyse gene regulation. Cullum R, Alder O, Hoodless PA, Respirology 2011 16 2 210 222 10.1111/j.1440-1843.2010.01899.x 21077988
16. Sequencing technologies-the next generation. Metzker ML, Nat Rev Genet 2010 11 1 31 46 10.1038/nrg2626 19997069
17. Genomes for All. Church M, Sci Am 2006 294 46 54 16596879
18. Advanced sequencing technologies and their wider impact in microbiology. Hall N, J Exp Biol 2007 210 Pt 9 1518 1525 17449817 (Pubitemid 46841957)
19. Sequencing and genome assembly using next-generation technologies. Nagarajan N, Pop M, Methods Mol Biol 2010 673 1 17 10.1007/978-1-60761-842-3-1 20835789
20. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C, RNA 2010 16 5 991 1006 10.1261/rna.1947110 20360395
21. Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Hert DG, Fredlake CP, Barron AE, Electrophoresis 2008 29 23 4618 4626 10.1002/elps.200800456 19053153
22. High-throughput oncogene mutation profiling in human cancer. Thomas RK, Baker AC, Debiasi RM, Winckler W, Laframboise T, Lin WM, Wang M, Feng W, Zander T, MacConaill L, et al. Nat Genet 2007 39 3 347 351 10.1038/ng1975 17293865 (Pubitemid 46328493)
23. Solexa Ltd. Bennett S, Pharmacogenomics 2004 5 4 433 438 10.1517/14622416.5.4.433 15165179 (Pubitemid 38923657)
24. Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. Nature 2008 456 7218 53 59 10.1038/nature07517 18987734
25. Genome sequencing in microfabricated high-density picolitre reactors. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Nature 2005 437 7057 376 380 16056220 (Pubitemid 41613494)
26. Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT, PLoS One 2012 7 2 30087 10.1371/journal.pone.0030087 22347999
27. Comparison of next-generation sequencing systems. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M, J Biomed Biotechnol 2012 2012 251364 22829749
28. Perspectives and challenges of emerging single-molecule DNA sequencing technologies. Xu M, Fujita D, Hanagata N, Small 2009 5 23 2638 2649 10.1002/smll.200900976 19904762
29. RNA-Seq: a revolutionary tool for transcriptomics. Wang Z, Gerstein M, Snyder M, Nat Rev Genet 2009 10 1 57 63 10.1038/nrg2484 19015660
30. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M, Biotechniques 2008 45 1 81 94 10.2144/000112900 18611170
31. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Furey TS, Nat Rev Genet 2012 13 12 840 852 10.1038/nrg3306 23090257
32. A whole-genome assembly of drosophila. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. Science 2000 287 5461 2196 2204 10.1126/science.287.5461.2196 10731133 (Pubitemid 30177014)
33. The atlas genome assembly system. Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA, Genome Res 2004 14 4 721 732 10.1101/gr.2264004 15060016 (Pubitemid 38500246)
34. ARACHNE: a whole-genome shotgun assembler. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES, Genome Res 2002 12 1 177 189 10.1101/gr.208902 11779843
35. Whole-genome shotgun assembly and analysis of the genome of fugu rubripes. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. Science 2002 297 5585 1301 1310 10.1126/science.1072104 12142439 (Pubitemid 34913162)
36. PCAP: a whole-genome assembly program. Huang X, Wang J, Aluru S, Yang SP, Hillier L, Genome Res 2003 13 9 2164 2170 10.1101/gr.1390403 12952883 (Pubitemid 37161773)
37. ABySS: a parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I, Genome Res 2009 19 6 1117 1123 10.1101/gr.089532.108 19251739
38. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 5 821 829 10.1101/gr.074492.107 18349386 (Pubitemid 351645072)
39. The phusion assembler. Mullikin JC, Ning Z, Genome Res 2003 13 1 81 90 10.1101/gr.731003 12529309
40. Database resources of the national center for biotechnology information. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Nucleic Acids Res 2007 35 Database issue 5 12 17170002
41. The human gene mutation database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN, Current protocols in bioinformatics, Baxevanis AD, 2012 Chapter 1:Unit1 13. PMID:22948725
42. HGBASE: a database of SNPs and other variations in and around human genes. Brookes AJ, Lehvaslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F, Nucleic Acids Res 2000 28 1 356 360 10.1093/nar/28.1.356 10592273 (Pubitemid 30047806)
43. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Fredman D, Siegfried M, Yuan YP, Bork P, Lehvaslaiho H, Brookes AJ, Nucleic Acids Res 2002 30 1 387 391 10.1093/nar/30.1.387 11752345 (Pubitemid 34679593)
44. The GWAS central http://www.gwascentral.org
45. The SNPedia http://www.snpedia.com/index.php/SNPedia
46. Next generation tools for the annotation of human SNPs. Karchin R, Brief Bioinform 2009 10 1 35 52 19181721
47. Computational methods for discovering structural variation with next-generation sequencing. Medvedev P, Stanciu M, Brudno M, Nat Methods 2009 6 11 Suppl 13 20 19844226
48. The sanger FASTQ file format for sequences with quality scores, and the solexa/illumina FASTQ variants. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM, Nucleic Acids Res 2010 38 6 1767 1771 10.1093/nar/gkp1137 20015970
49. Genome project data processing S: the sequence alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Bioinformatics 2009 25 16 2078 2079 10.1093/ bioinformatics/btp352 19505943
50. The variant call format and VCFtools. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. Bioinformatics 2011 27 15 2156 2158 10.1093/bioinformatics/btr330 21653522
51. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Ewing B, Hillier L, Wendl MC, Green P, Genome Res 1998 8 3 175 185 10.1101/gr.8.3.175 9521921 (Pubitemid 28177229)
52. A comprehensive catalogue of somatic mutations from a human cancer genome. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, et al. Nature 2010 463 7278 191 196 10.1038/nature08658 20016485
53. Compression of genomic sequences in FASTQ format. Deorowicz S, Grabowski S, Bioinformatics 2011 PMID: 21252073
54. G-SQZ: compact encoding of genomic sequence and quality data. Tembe W, Lowey J, Suh E, Bioinformatics 2010 26 17 2192 2194 10.1093/bioinformatics/ btq346 20605925
55. Biopython: freely available python tools for computational molecular biology and bioinformatics. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, et al. Bioinformatics 2009 25 11 1422 1423 10.1093/bioinformatics/btp163 19304878
56. The bioperl toolkit: perl modules for the life sciences. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, et al. Genome Res 2002 12 10 1611 1618 10.1101/gr.361602 12368254 (Pubitemid 35175100)
57. BioRuby: bioinformatics software for the ruby programming language. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T, Bioinformatics 2010 26 20 2617 2619 10.1093/bioinformatics/btq475 20739307
58. The sequence alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Bioinformatics 2009 25 16 2078 2079 10.1093/bioinformatics/btp352 19505943
59. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Botstein D, Risch N, Nat Genet 2003 33 Suppl 228 237 12610532 (Pubitemid 36278833)
60. Genetic mapping in human disease. Altshuler D, Daly MJ, Lander ES, Science 2008 322 5903 881 888 10.1126/science.1156409 18988837
61. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. Nat Methods 2009 6 9 677 681 10.1038/nmeth.1363 19668202
62. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Xie C, Tammi MT, BMC Bioinforma 2009 10 80 10.1186/1471-2105-10-80
63. A geometric approach for classification and comparison of structural variants. Sindi S, Helman E, Bashir A, Raphael BJ, Bioinformatics 2009 25 12 222 230 10.1093/bioinformatics/btp208 19477992
64. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM, Genome Res 2010 20 5 623 635 10.1101/gr.102970.109 20308636
65. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Lee S, Hormozdiari F, Alkan C, Brudno M, Nat Methods 2009 6 7 473 474 10.1038/nmeth.f.256 19483690
66. mrsFAST: a cache-oblivious algorithm for short-read mapping. Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC, Nat Methods 2010 7 8 576 577 10.1038/nmeth0810-576 20676076
67. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC, Bioinformatics 2010 26 10 1277 1283 10.1093/bioinformatics/btq152 20385726
68. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB, Genome Biol 2009 10 2 23 10.1186/gb-2009-10-2-r23 19236709
69. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z, Bioinformatics 2009 25 21 2865 2871 10.1093/bioinformatics/btp394 19561018
70. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. Kim TM, Luquette LJ, Xi R, Park PJ, BMC Bioinforma 2010 11 432 10.1186/1471-2105-11-432
71. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC, Bioinformatics 2010 26 12 350 357 10.1093/bioinformatics/btq216 20529927
72. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK, Genome Res 2012 22 3 568 576 10.1101/gr.129684.111 22300766
73. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L, Bioinformatics 2009 25 17 2283 2285 10.1093/bioinformatics/btp373 19542151
74. Genetic heterogeneity in human disease. McClellan J, King MC, Cell 2010 141 2 210 217 10.1016/j.cell.2010.03.032 20403315
75. Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Cantor RM, Lange K, Sinsheimer JS, Am J Hum Genet 2010 86 1 6 22 10.1016/j.ajhg.2009.11.017 20074509
76. Annotate-it: a swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y, Aerts J, Genome Med 2012 4 9 73 10.1186/gm374 23013645
77. A comprehensive framework for prioritizing variants in exome sequencing studies of mendelian diseases. Li MX, Gui HS, Kwan JS, Bao SY, Sham PC, Nucleic Acids Res 2012 40 7 53 10.1093/nar/gkr1257 22241780
78. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Wang K, Li M, Hakonarson H, Nucleic Acids Res 2010 38 16 164 10.1093/nar/gkq603 20601685
79. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants. Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S, Bioinformatics 2012 28 5 724 725 10.1093/bioinformatics/bts032 22257670
80. SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. Shetty AC, Athri P, Mondal K, Horner VL, Steinberg KM, Patel V, Caspary T, Cutler DJ, Zwick ME, BMC Bioinforma 2010 11 471 10.1186/1471-2105-11- 471
81. SVA: software for annotating and visualizing sequenced human genomes. Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, Heinzen EL, Need AC, Cirulli ET, Maia JM, Dickson SP, et al. Bioinformatics 2011 27 14 1998 2000 10.1093/ bioinformatics/btr317 21624899
82. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, et al. Bioinformatics 2012 28 2 277 278 10.1093/bioinformatics/btr612 22088845
83. A probabilistic disease-gene finder for personal genomes. Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG, Genome Res 2011 21 9 1529 1542 10.1101/gr.123158.111 21700766
84. VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. Cheng YC, Hsiao FC, Yeh EC, Lin WJ, Tang CY, Tseng HC, Wu HT, Liu CK, Chen CC, Chen YT, et al. Nucleic Acids Res 2012 40 Web Server issue 76 81 22618869
85. VAR-MD: a tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance. Sincan M, Simeonov DR, Adams D, Markello TC, Pierson TM, Toro C, Gahl WA, Boerkoel CF, Hum Mutat 2012 33 4 593 598 10.1002/humu.22034 22290570
86. VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Teer JK, Green ED, Mullikin JC, Biesecker LG, Bioinformatics 2012 28 4 599 600 10.1093/bioinformatics/btr711 22210868
87. Visualizing biological data-now and in the future. O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Heriche JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, et al. Nat Methods 2010 7 3 Suppl 2 4 20195254
88. ABySS-explorer: visualizing genome sequence assemblies. Nielsen CB, Jackman SD, Birol I, Jones SJ, IEEE Trans Vis Comput Graph 2009 15 6 881 888 19834150
89. EagleView: a genome assembly viewer for next-generation sequencing technologies. Huang W, Marth G, Genome Res 2008 18 9 1538 1543 10.1101/gr.076067.108 18550804
90. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M, Brief Bioinform 2013 14 2 213 224 10.1093/bib/bbr074 22199379
91. LookSeq: a browser-based viewer for deep sequencing data. Manske HM, Kwiatkowski DP, Genome Res 2009 19 11 2125 2132 10.1101/gr.093443.109 19679872
92. MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. Hou H, Zhao F, Zhou L, Zhu E, Teng H, Li X, Bao Q, Wu J, Sun Z, Nucleic Acids Res 2010 38 Web Server issue 732 736 20444865
93. MapView: visualization of short reads alignment on a desktop computer. Bao H, Guo H, Wang J, Zhou R, Lu X, Shi S, Bioinformatics 2009 25 12 1554 1555 10.1093/bioinformatics/btp255 19369497
94. Comparison of human (and other) genome browsers. Furey TS, Hum Genomics 2006 2 4 266 270 10.1186/1479-7364-2-4-266 16460652 (Pubitemid 43192230)
95. Understanding genome browsing. Cline MS, Kent WJ, Nat Biotechnol 2009 27 2 153 155 10.1038/nbt0209-153 19204697
96. Visualizing genomes: techniques and challenges. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T, Nat Methods 2010 7 3 Suppl 5 S15 20195257
97. AnnoJ http://www.annoj.org
98. The CGView server: a comparative genomics tool for circular genomes. Grant JR, Stothard P, Nucleic Acids Res 2008 36 Web Server issue 181 184 18411202
99. Combo: a whole genome comparative browser. Engels R, Yu T, Burge C, Mesirov JP, DeCaprio D, Galagan JE, Bioinformatics 2006 22 14 1782 1783 10.1093/bioinformatics/btl193 16709588 (Pubitemid 44288342)
100. Ensembl 2012. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. Nucleic Acids Res 2012 40 Database issue 84 90 22086963
101. The ensembl genome database project. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, et al. Nucleic Acids Res 2002 30 1 38 41 10.1093/nar/30.1.38 11752248 (Pubitemid 34679498)
102. The GMOD drupal bioinformatic server framework. Papanicolaou A, Heckel DG, Bioinformatics 2010 26 24 3119 3124 10.1093/bioinformatics/btq599 20971988
103. SynView: a GBrowse-compatible approach to visualizing comparative genome data. Wang H, Su Y, Mackey AJ, Kraemer ET, Kissinger JC, Bioinformatics 2006 22 18 2308 2309 10.1093/bioinformatics/btl389 16844709 (Pubitemid 44390889)
104. The generic genome browser: a building block for a model organism system database. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, et al. Genome Res 2002 12 10 1599 1610 10.1101/gr.403602 12368253 (Pubitemid 35175099)
105. Genome projector: zoomable genome map with multiple views. Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M, BMC Bioinforma 2009 10 31 10.1186/1471-2105-10-31
106. The integrated genome browser: free software for distribution and exploration of genome-scale datasets. Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE, Bioinformatics 2009 25 20 2730 2731 10.1093/bioinformatics/btp472 19654113
107. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Thorvaldsdottir H, Robinson JT, Mesirov JP, Brief Bioinform 2013 14 2 178 192 10.1093/bib/bbs017 22517427
108. The UCSC cancer genomics browser. Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, et al. Nat Methods 2009 6 4 239 240 10.1038/nmeth0409-239 19333237
109. The human genome browser at UCSC. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D, Genome Res 2002 12 6 996 1006 12045153 (Pubitemid 34662293)
110. X:Map: annotation and visualization of genome structure for affymetrix exon array analysis. Yates T, Okoniewski MJ, Miller CJ, Nucleic Acids Res 2008 36 Database issue 780 786 17932061
111. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. Sinha AU, Meller J, BMC Bioinforma 2007 8 82 10.1186/1471-2105-8-82 (Pubitemid 46443805)
112. Ggbio: an R package for extending the grammar of graphics for genomic data. Yin T, Cook D, Lawrence M, Genome Biol 2012 13 8 77 10.1186/gb-2012-13-8- r77 22937822
113. GenomeComp: a visualization tool for microbial genome comparison. Yang J, Wang J, Yao ZJ, Jin Q, Shen Y, Chen R, J Microbiol Methods 2003 54 3 423 426 10.1016/S0167-7012(03)00094-0 12842490 (Pubitemid 36773985)
114. Circos: an information aesthetic for comparative genomics. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA, Genome Res 2009 19 9 1639 1645 10.1101/gr.092759.109 19541911
115. DHPC: a new tool to express genome structural features. Deng X, Rayner S, Liu X, Zhang Q, Yang Y, Li N, Genomics 2008 91 5 476 483 10.1016/j.ygeno.2008. 01.003 18343093
116. Visualization of genomic data with the hilbert curve. Anders S, Bioinformatics 2009 25 10 1231 1235 PMID: 23605045 10.1093/bioinformatics/btp152 19297348
117. InGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Qi J, Zhao F, Nucleic Acids Res 2011 39 Web Server issue 567 575 21715388
118. Meander: visually exploring the structural variome using space-filling curves. Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J, Nucleic Acids Res 2013
119. MEDEA, Comparative genomic visualization with adobe flash [ http://www.broadinstitute.org/annotation/medea/ ]
120. MizBee: a multiscale synteny browser. Meyer M, Munzner T, Pfister H, IEEE Trans Vis Comput Graph 2009 15 6 897 904 19834152
121. Seevolution: visualizing chromosome evolution. Esteban-Marcos A, Darling AE, Ragan MA, Bioinformatics 2009 25 7 960 961 10.1093/bioinformatics/btp096 19233896
122. Sybil: methods and software for multiple genome comparison and visualization. Crabtree J, Angiuoli SV, Wortman JR, White OR, Methods Mol Biol 2007 408 93 108 Clifton, NJ 10.1007/978-1-59745-547-3-6 18314579
123. VISTA: visualizing global DNA sequence alignments of arbitrary length. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I, Bioinformatics 2000 16 11 1046 1047 10.1093/bioinformatics/16.11.1046 11159318 (Pubitemid 32051021)
124. A reference guide for tree analysis and visualization. Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R, BioData Min 2010 3 1 1 10.1186/1756-0381-3-1 20175922
125. A survey of visualization tools for biological network analysis. Pavlopoulos GA, Wegener AL, Schneider R, BioData Min 2008 1 12 10.1186/1756-0381-1-12 19040716