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Transposable element detection from whole genome sequence data

Ewing, Adam D.·2015·Mobile DNA
DOI 10.1186/s13100-015-0055-3PMC PMC4696183
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Fig. 1 Read mapping patterns typically associated with insertion detection. Panel a shows the read mapping patterns versus a reference TE sequence (grey rectangle, top) and the mapping of the same reads to a reference genome sequence (orange rectangle, bottom). Reads are represented as typical paired-end reads where the ends of each amplicon are represented as rectangles and the un-sequenced portion of the amplicons are represented as bars connecting the rectangles. Reads informative for identifying TE insertion locations are indicated by dashed boxes, other read mappings to the TE reference are shown in light blue boxes. Within the informative reads, reads or portions of reads mapping to the TE reference are coloured blue, and mappings to the reference genome sequence are coloured yellow. The exact location of this example insertion is indicated by the red triangle and the dashed line. Assembly of the reads supporting the two junction sequences is indicated to the right of the ‘consensus’ arrow, one example with a TSD and one without. If a TSD is present, the insertion breakends relative to the reference genome are staggered, and the overlap of reference-aligned sequence corresponds to the TSD. If a TSD is not present (and no bases are deleted upon insertion), the junctions obtained from the 5' end and the 3' end of the TE reference will match exactly. Panel b shows a typical pattern of discordant read mappings across a genome - the colored segments in circle represent chromosomes, each black link indicates a discordant read mapping supporting an insertion at the position indicated by the red triangle. The endpoints not corresponding to the insertion site map to TE elements at various locations in the reference genome
Fig. 1 Read mapping patterns typically associated with insertion detection. Panel a shows the read mapping patterns versus a reference TE sequence (grey rectangle, top) and the mapping of the same reads to a reference genome sequence (orange rectangle, bottom). Reads are represented as typical paired-end reads where the ends of each amplicon are represented as rectangles and the un-sequenced portion of the amplicons are represented as bars connecting the rectangles. Reads informative for identifying TE insertion locations are indicated by dashed boxes, other read mappings to the TE reference are shown in light blue boxes. Within the informative reads, reads or portions of reads mapping to the TE reference are coloured blue, and mappings to the reference genome sequence are coloured yellow. The exact location of this example insertion is indicated by the red triangle and the dashed line. Assembly of the reads supporting the two junction sequences is indicated to the right of the ‘consensus’ arrow, one example with a TSD and one without. If a TSD is present, the insertion breakends relative to the reference genome are staggered, and the overlap of reference-aligned sequence corresponds to the TSD. If a TSD is not present (and no bases are deleted upon insertion), the junctions obtained from the 5' end and the 3' end of the TE reference will match exactly. Panel b shows a typical pattern of discordant read mappings across a genome - the colored segments in circle represent chromosomes, each black link indicates a discordant read mapping supporting an insertion at the position indicated by the red triangle. The endpoints not corresponding to the insertion site map to TE elements at various locations in the reference genomeCC BY · PubMed Central
Fig. 2 Intersections between somatic insertion detection methods. Overlap and non-overlap between insertion sites from reported in publications using the indicated software tools on the same data. The number of samples included in the comparison shared between the each pair of studies is indicated
Fig. 2 Intersections between somatic insertion detection methods. Overlap and non-overlap between insertion sites from reported in publications using the indicated software tools on the same data. The number of samples included in the comparison shared between the each pair of studies is indicatedCC BY · PubMed Central

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Research works printed but not linked: 83

  1. Kazazian HH, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988;332(6160):164–6. doi: 10.1038/332164a0 . · DOI
  2. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921. doi: 10.1038/35057062 . · DOI · Paper page
  3. Cordaux R, Hedges DJ, Herke SW, Batzer MA. Estimating the retrotransposition rate of human Alu elements. Gene. 2006;373:134–7. doi: 10.1016/j.gene.2006.01.019 . · DOI
  4. Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, et al. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 2009;19(9):1516–26. doi: 10.1101/gr.091827.109 . · DOI
  5. Ewing AD, Kazazian HH. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 2010;20(9):1262–70. doi: 10.1101/gr.106419.110 . · DOI
  6. Huang CRL, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, et al. Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010;141(7):1171–82. doi: 10.1016/j.cell.2010.05.026 . · DOI
  7. Faulkner GJ. Retrotransposons: mobile and mutagenic from conception to death. FEBS Lett. 2011;585(11):1589–94. doi: 10.1016/j.febslet.2011.03.061 . · DOI
  8. Xing J, Witherspoon DJ, Jorde LB. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet. 2013;29(5):280–9. doi: 10.1016/j.tig.2012.12.002 . · DOI
  9. Bergman CM, Quesneville H. Discovering and detecting transposable elements in genome sequences. Brief Bioinformatics. 2007;8(6):382–92. doi: 10.1093/bib/bbm048 . · DOI
  10. Saha S, Bridges S, Magbanua ZV, Peterson DG. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Res. 2008;36(7):2284–94. doi: 10.1093/nar/gkn064 . · DOI
  11. Cordaux R, Sen SK, Konkel MK, Batzer MA. Computational methods for the analysis of primate mobile elements. Methods Mol Biol. 2010;628:137–51. doi: 10.1007/978-1-60327-367-1 . · DOI
  12. Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity. 2010;104(6):520–33. doi: 10.1038/hdy.2009.165 . · DOI
  13. Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, et al. A call for benchmarking transposable element annotation methods. Mob DNA. 2015;6:13. doi: 10.1186/s13100-015-0044-6 . · DOI · Paper page
  14. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007;318(5849):420–6. doi: 10.1126/science.1149504 . · DOI · Paper page
  15. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 1993;72(4):595–605. doi: 10.1016/0092-8674(93)90078-5 . · DOI · Paper page
  16. Roy-Engel AM, Salem A-H, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, et al. Active Alu Element “A-Tails”: Size Does Matter. Genome Res. 2002;12(9):1333–44. doi: 10.1101/gr.384802 . · DOI
  17. Dewannieux M, Heidmann T. Role of poly(A) tail length in Alu retrotransposition. Genomics. 2005;86(3):378–81. doi: 10.1016/j.ygeno.2005.05.009 . · DOI
  18. Dai L, Taylor MS, O’Donnell KA, Boeke JD. Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. Mol Cell Biol. 2012;32(21):4323–36. doi: 10.1128/MCB.06785-11 . · DOI
  19. Doucet A, Wilusz J, Miyoshi T, Liu Y, Moran J. A 3’ poly(a) tract is required for line-1 retrotransposition. Mol Cell. 2015. doi: 10.1016/j.molcel.2015.10.012 . · DOI
  20. Fuhrman SA, Deininger PL, LaPorte P, Friedmann T, Geiduschek EP. Analysis of transcription of the human Alu family ubiquitous repeating element by eukaryotic RNA polymerase III. Nucleic Acids Res. 1981;9(23):6439–56. doi: 10.1093/nar/9.23.6439 . · DOI
  21. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH. High frequency retrotransposition in cultured mammalian cells. Cell. 1996;87(5):917–27. · DOI · Paper page
  22. Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat Gen. 2000;24(4):363–7. doi: 10.1038/74184 . · DOI
  23. Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003;13(12):2541–58. doi: 10.1101/gr.1429003 . · DOI
  24. Kazazian HH, Moran JV. The impact of L1 retrotransposons on the human genome. Nat Genet. 1998;19(1):19–24. doi: 10.1038/ng0598-19 . · DOI
  25. Lucier J-F, Perreault J, Noël J-F, Boire G, Perreault J-P. RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. Nucleic Acids Res. 2007;35 suppl 2:269–74. doi: 10.1093/nar/gkm313 . · DOI
  26. Gilbert N, Lutz-Prigge S, Moran JV. Genomic deletions created upon LINE-1 retrotransposition. Cell. 2002;110(3):315–25. doi: 10.1016/S0092-8674(02)00828-0 . · DOI · Paper page
  27. Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, et al. Human l1 retrotransposition is associated with genetic instability in vivo. Cell. 2002;110(3):327–38. doi: 10.1016/S0092-8674(02)00839-5 . · DOI
  28. Morrish TA, Garcia-Perez JL, Stamato TD, Taccioli GE, Sekiguchi J, Moran JV. Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres. Nature. 2007;446(7132):208–12. doi: 10.1038/nature05560 . · DOI
  29. Moran JV, DeBerardinis RJ, Kazazian HH. Exon shuffling by L1 retrotransposition. Science. 1999;283(5407):1530–4. doi: 10.1126/science.283.5407.1530 . · DOI
  30. Goodier JL, Ostertag EM, Kazazian HH. Transduction of 3’-flanking sequences is common in L1 retrotransposition. Hum Mol Genet. 2000;9(4):653–7. doi: 10.1093/hmg/9.4.653 . · DOI
  31. Pickeral OK, Makalowski W, Boguski MS, Boeke JD. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 2000;10(4):411–5. doi: 10.1101/gr.10.4.411 . · DOI
  32. Grimaldi G, Skowronski J, Singer MF. Defining the beginning and end of KpnI family segments. EMBO J. 1984;3(8):1753–9. · DOI
  33. Pavlı́cek A, Paces J, Zı́ka R, Hejnar J. Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. Gene. 2002;300(1-2):189–94. doi: 10.1016/S0378-1119(02)01047-8 . · DOI
  34. Solyom S, Ewing AD, Hancks DC, Takeshima Y, Awano H, Matsuo M, et al. Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon. Hum Mutat. 2012;33(2):369–71. doi: 10.1002/humu.21663 . · DOI
  35. Ostertag EM, Kazazian HH. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 2001;11(12):2059–65. doi: 10.1101/gr.205701 . · DOI
  36. Hénaff E, Zapata L, Casacuberta JM, Ossowski S. Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. BMC genomics. 2015;16(1):768. doi: 10.1186/s12864-015-1975-5 . · DOI
  37. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio]. 2013; arXiv: 1303.3997 · arXiv
  38. Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002;12(4):656–64. doi: 10.1101/gr.229202 . · DOI · Paper page
  39. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21(3):487–93. doi: 10.1101/gr.113985.110 . · DOI
  40. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10. doi: 10.1016/S0022-2836(05)80360-2 . · DOI · Paper page
  41. Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, et al. Fast computation and applications of genome mappability. PLoS ONE. 2012;7(1):30377. doi: 10.1371/journal.pone.003037 . · DOI
  42. Lee H, Schatz MC. Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics. 2012;28(16):2097–105. doi: 10.1093/bioinformatics/bts330 . · DOI
  43. Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat. 2006;27(4):323–9. doi: 10.1002/humu.20307 . · DOI
  44. Mir AA, Philippe C, Cristofari G. euL1db: the European database of L1hs retrotransposon insertions in humans. Nucleic Acids Res. 2015;43(Database issue):43–7. doi: 10.1093/nar/gku1043 . · DOI · Paper page
  45. Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013;29(3):389–90. doi: 10.1093/bioinformatics/bts697 . · DOI
  46. Nellåker C, Keane TM, Yalcin B, Wong K, Agam A, Belgard TG, et al. The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol. 2012;13(6):45. doi: 10.1186/gb-2012-13-6-r45 . · DOI
  47. Fiston-Lavier A-S, Carrigan M, Petrov DA, González J. T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res. 2011;39(6):36. doi: 10.1093/nar/gkq1291 . · DOI
  48. Fiston-Lavier A-S, Barrón MG, Petrov DA, González J. T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Res. 2015;43(4):22. doi: 10.1093/nar/gku1250 . · DOI
  49. Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD. Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Res. 2012;22(4):693–703. doi: 10.1101/gr.129460.111 . · DOI
  50. Guo Y, Levin HL. High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe. Genome Res. 2010;20(2):239–48. doi: 10.1101/gr.099648.109 . · DOI
  51. Gangadharan S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo. Proc Nat Acad Sci. 2010;107(51):21966–72. doi: 10.1073/pnas.1016382107 . · DOI
  52. Xiong Y, Eickbush TH. The site-specific ribosomal DNA insertion element R1bm belongs to a class of non-long-terminal-repeat retrotransposons. Mol Cell Biol. 1988;8(1):114–23. doi: 10.1128/MCB.8.1.114 . · DOI
  53. Han M-J, Xu H-E, Zhang H-H, Feschotte C, Zhang Z. Spy: a new group of eukaryotic DNA transposons without target site duplications. Genome Biol Evol. 2014;6(7):1748–57. doi: 10.1093/gbe/evu140 . · DOI
  54. McClintock B. The origin and behavior of mutable loci in maize. Proc Nat Acad Sci USA. 1950;36(6):344–55. · DOI
  55. Sutton WD, Gerlach WL, Peacock WJ, Schwartz D. Molecular analysis of ds controlling element mutations at the adh1 locus of maize. Science (New York, NY). 1984;223(4642):1265–8. doi: 10.1126/science.223.4642.1265 . · DOI
  56. Döring HP, Tillmann E, Starlinger P. DNA sequence of the maize transposable element Dissociation. Nature. 1984;307(5947):127–30. doi: 10.1038/307127a0 . · DOI
  57. O’Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013;5(3):28. doi: 10.1186/gm432 . · DOI
  58. Kim SY, Speed TP. Comparing somatic mutation-callers: beyond Venn diagrams. BMC Bioinformatics. 2013;14:189. doi: 10.1186/1471-2105-14-189 . · DOI
  59. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al. ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen, M.R., Norman, T.C., Haussler, D., Friend, S.H., Stolovitzky, G., Margolin, A.A., Stuart, J.M., Boutros, P.C.: Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015;12(7):623–30. doi: 10.1038/nmeth.3407 . · DOI
  60. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, et al. Cancer Genome Atlas Research Network: Landscape of somatic retrotransposition in human cancers. Science. 2012;337(6097):967–71. doi: 10.1126/science.1222077 . · DOI · Paper page
  61. Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345(6196):1251343. doi: 10.1126/science.1251343 . · DOI · Paper page
  62. Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature. 2015;517(7536):608–11. doi: 10.1038/nature13907 . · DOI
  63. Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015;12(8):733–5. doi: 10.1038/nmeth.3444 . · DOI
  64. Ammar R, Paton TA, Torti D, Shlien A, Bader GD. Long read nanopore sequencing for detection of HLA and CYP2d6 variants and haplotypes. F1000Research. 2015. doi: 10.12688/f1000research.6037.2 . · DOI
  65. Madoui M-A, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics. 2015;16:327. doi: 10.1186/s12864-015-1519-z . · DOI
  66. Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat Meth. 2015;12(4):351–6. doi: 10.1038/nmeth.3290 . · DOI
  67. Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, et al. SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics. 2014;30(19):2787–95. doi: 10.1093/bioinformatics/btu345 . · DOI
  68. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) — round x. Proteins: Struct Funct Bioinf. 2014;82:1–6. doi: 10.1002/prot.24452 . · DOI
  69. Wu J, Lee W-P, Ward A, Walker JA, Konkel MK, Batzer MA, et al. Tangram: a comprehensive toolbox for mobile element insertion detection. BMC Genomics. 2014;15:795. doi: 10.1186/1471-2164-15-795 . · DOI
  70. Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, et al. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics. 2010;26(12):350–7. doi: 10.1093/bioinformatics/btq216 . · DOI
  71. Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, et al. Alu repeat discovery and characterization within human genomes. Genome Res. 2011;21(6):840–9. doi: 10.1101/gr.115956.110 . · DOI
  72. Ewing AD, Ballinger TJ, Earl D, Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013;14(3):22. doi: 10.1186/gb-2013-14-3-r22 . · DOI
  73. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, et al. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 2010;20(5):623–35. doi: 10.1101/gr.102970.109 . · DOI
  74. Robb SMC, Lu L, Valencia E, Burnette JM, Okumoto Y, Wessler SR, et al. The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3 (Bethesda). 2013;3(6):949–57. doi: 10.1534/g3.112.005348 . · DOI
  75. Jiang C, Chen C, Huang Z, Liu R, Verdier J. ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics. 2015;16:72. doi: 10.1186/s12859-015-0507-2 . · DOI
  76. Linheiro RS, Bergman CM. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS ONE. 2012;7(2):30008. doi: 10.1371/journal.pone.0030008 . · DOI
  77. Platzer A, Nizhynska V, Long Q. TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology (Basel). 2012;1(2):395–410. doi: 10.3390/biology1020395 . · DOI
  78. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 2014;24(2):310–7. doi: 10.1101/gr.162883.113 . · DOI
  79. Thung DT, de Ligt J, Vissers LEM, Steehouwer M, Kroon M, de Vries P, et al. Mobster: accurate detection of mobile element insertions in next generation sequencing data. Genome Biol. 2014;15(10):488. doi: 10.1186/s13059-014-0488-x . · DOI
  80. Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res. 2014;42(11):6826–38. doi: 10.1093/nar/gku323 . · DOI
  81. Gilly A, Etcheverry M, Madoui M-A, Guy J, Quadrana L, Alberti A, et al. TE-Tracker: systematic identification of transposition events through whole-genome resequencing. BMC Bioinformatics. 2014;15:377. doi: 10.1186/s12859-014-0377-z . · DOI
  82. Kroon M, Lameijer EW, Lakenberg N, Hehir-Kwa JY, Thung DT, Slagboom PE, et al. Detecting dispersed duplications in high-throughput sequencing data using a database-free approach. Bioinformatics. 2015; 621. doi: 10.1093/bioinformatics/btv621 · DOI
  83. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526:75–81. doi: 10.1038/nature15394 . · DOI · Paper page

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Metadata

Authors
Ewing, A. D.
Venue
Mobile DNA
Publisher
Springer Science and Business Media LLC
Published
2015-12
Volume
6
Issue
1
ISSN
1759-8753
DOI
10.1186/s13100-015-0055-3
PMC
PMC4696183
Cited by
155
References
6
Language
en
Licence
Funders
  • Australian Research Council (DE150101117)
  • Mater Foundation

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