ruby-minigraph 0.0.20.0

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  1. checksums.yaml +7 -0
  2. data/LICENSE.txt +21 -0
  3. data/README.md +62 -0
  4. data/ext/Rakefile +56 -0
  5. data/ext/cmappy/cmappy.c +7 -0
  6. data/ext/cmappy/cmappy.h +8 -0
  7. data/ext/minigraph/LICENSE.txt +23 -0
  8. data/ext/minigraph/Makefile +66 -0
  9. data/ext/minigraph/NEWS.md +317 -0
  10. data/ext/minigraph/README.md +207 -0
  11. data/ext/minigraph/algo.c +194 -0
  12. data/ext/minigraph/algo.h +33 -0
  13. data/ext/minigraph/asm-call.c +147 -0
  14. data/ext/minigraph/bseq.c +133 -0
  15. data/ext/minigraph/bseq.h +76 -0
  16. data/ext/minigraph/cal_cov.c +139 -0
  17. data/ext/minigraph/doc/example1.png +0 -0
  18. data/ext/minigraph/doc/example2.png +0 -0
  19. data/ext/minigraph/doc/examples.graffle +0 -0
  20. data/ext/minigraph/format.c +241 -0
  21. data/ext/minigraph/galign.c +140 -0
  22. data/ext/minigraph/gchain1.c +532 -0
  23. data/ext/minigraph/gcmisc.c +223 -0
  24. data/ext/minigraph/gfa-aug.c +260 -0
  25. data/ext/minigraph/gfa-base.c +526 -0
  26. data/ext/minigraph/gfa-bbl.c +372 -0
  27. data/ext/minigraph/gfa-ed.c +617 -0
  28. data/ext/minigraph/gfa-io.c +395 -0
  29. data/ext/minigraph/gfa-priv.h +154 -0
  30. data/ext/minigraph/gfa.h +166 -0
  31. data/ext/minigraph/ggen.c +182 -0
  32. data/ext/minigraph/ggen.h +21 -0
  33. data/ext/minigraph/ggsimple.c +570 -0
  34. data/ext/minigraph/gmap.c +211 -0
  35. data/ext/minigraph/index.c +230 -0
  36. data/ext/minigraph/kalloc.c +224 -0
  37. data/ext/minigraph/kalloc.h +82 -0
  38. data/ext/minigraph/kavl.h +414 -0
  39. data/ext/minigraph/kdq.h +134 -0
  40. data/ext/minigraph/ketopt.h +116 -0
  41. data/ext/minigraph/khashl.h +348 -0
  42. data/ext/minigraph/krmq.h +474 -0
  43. data/ext/minigraph/kseq.h +256 -0
  44. data/ext/minigraph/ksort.h +164 -0
  45. data/ext/minigraph/kstring.h +165 -0
  46. data/ext/minigraph/kthread.c +159 -0
  47. data/ext/minigraph/kthread.h +15 -0
  48. data/ext/minigraph/kvec-km.h +105 -0
  49. data/ext/minigraph/kvec.h +110 -0
  50. data/ext/minigraph/lchain.c +441 -0
  51. data/ext/minigraph/main.c +301 -0
  52. data/ext/minigraph/map-algo.c +500 -0
  53. data/ext/minigraph/mgpriv.h +128 -0
  54. data/ext/minigraph/minigraph.1 +359 -0
  55. data/ext/minigraph/minigraph.h +176 -0
  56. data/ext/minigraph/miniwfa.c +834 -0
  57. data/ext/minigraph/miniwfa.h +95 -0
  58. data/ext/minigraph/misc/mgutils.js +1451 -0
  59. data/ext/minigraph/misc.c +12 -0
  60. data/ext/minigraph/options.c +134 -0
  61. data/ext/minigraph/shortk.c +251 -0
  62. data/ext/minigraph/sketch.c +109 -0
  63. data/ext/minigraph/sys.c +147 -0
  64. data/ext/minigraph/sys.h +20 -0
  65. data/ext/minigraph/test/MT-chimp.fa +277 -0
  66. data/ext/minigraph/test/MT-human.fa +239 -0
  67. data/ext/minigraph/test/MT-orangA.fa +276 -0
  68. data/ext/minigraph/test/MT.gfa +19 -0
  69. data/ext/minigraph/tex/Makefile +13 -0
  70. data/ext/minigraph/tex/minigraph.bib +676 -0
  71. data/ext/minigraph/tex/minigraph.tex +986 -0
  72. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp +42 -0
  73. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl +13 -0
  74. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp +269 -0
  75. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh +7 -0
  76. data/ext/minigraph/tex/plots/CHM13v1.cen.bed +23 -0
  77. data/ext/minigraph/tex/plots/CHM13v1.size +23 -0
  78. data/ext/minigraph/tex/plots/anno2tbl.js +40 -0
  79. data/ext/minigraph/tex/plots/bedutils.js +367 -0
  80. data/ext/minigraph/tex/plots/chr-plot.js +130 -0
  81. data/ext/minigraph/tex/plots/gen-anno.mak +24 -0
  82. data/ext/minigraph.patch +21 -0
  83. data/lib/minigraph/ffi/constants.rb +230 -0
  84. data/lib/minigraph/ffi/functions.rb +70 -0
  85. data/lib/minigraph/ffi/mappy.rb +8 -0
  86. data/lib/minigraph/ffi.rb +27 -0
  87. data/lib/minigraph/version.rb +5 -0
  88. data/lib/minigraph.rb +72 -0
  89. metadata +159 -0
@@ -0,0 +1,676 @@
1
+ @article{Schneider:2017aa,
2
+ Author = {Schneider, Valerie A and Graves-Lindsay, Tina and Howe, Kerstin and Bouk, Nathan and Chen, Hsiu-Chuan and Kitts, Paul A and Murphy, Terence D and Pruitt, Kim D and Thibaud-Nissen, Fran{\c c}oise and Albracht, Derek and Fulton, Robert S and Kremitzki, Milinn and Magrini, Vincent and Markovic, Chris and McGrath, Sean and Steinberg, Karyn Meltz and Auger, Kate and Chow, William and Collins, Joanna and Harden, Glenn and Hubbard, Timothy and Pelan, Sarah and Simpson, Jared T and Threadgold, Glen and Torrance, James and Wood, Jonathan M and Clarke, Laura and Koren, Sergey and Boitano, Matthew and Peluso, Paul and Li, Heng and Chin, Chen-Shan and Phillippy, Adam M and Durbin, Richard and Wilson, Richard K and Flicek, Paul and Eichler, Evan E and Church, Deanna M},
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+ Pages = {849-864},
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+ Title = {Evaluation of {GRCh38} and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly},
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+ Volume = {27},
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+ Year = {2017}}
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+ @article{Li:2018aa,
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+ Journal = {Genome Res},
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+ Year = {2017}}
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+ @article{Eichler_2010,
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+ Issn = {1546-1696},
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+ Journal = {Nature Biotechnology},
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+ Month = {Aug},
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+ Pages = {1155--1162},
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+ Publisher = {Springer Science and Business Media LLC},
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+ Title = {Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome},
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+ Volume = {37},
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+ Year = {2019}}
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+
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+ @article{Audano:2019aa,
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+ Author = {Audano, Peter A and Sulovari, Arvis and Graves-Lindsay, Tina A and Cantsilieris, Stuart and Sorensen, Melanie and Welch, AnneMarie E and Dougherty, Max L and Nelson, Bradley J and Shah, Ankeeta and Dutcher, Susan K and Warren, Wesley C and Magrini, Vincent and McGrath, Sean D and Li, Yang I and Wilson, Richard K and Eichler, Evan E},
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+ Journal = {Cell},
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+ Title = {Characterizing the Major Structural Variant Alleles of the Human Genome},
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+ Volume = {176},
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+ Year = {2019}}
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+ Year = {2019}}
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+ @article{Makinen:2010aa,
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+ Volume = {17},
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+ @article{Liu_2016,
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+ Title = {{deBWT}: parallel construction of {Burrows}--{Wheeler} {Transform} for large collection of genomes with de Bruijn-branch encoding},
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+ Volume = {32},
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+ Year = {2016}}
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+ @article{NA2016159,
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+ Title = {{FM-index} of alignment: A compressed index for similar strings},
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+ Volume = {638},
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+ Year = {2016}}
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+
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+ @article{cpgc:2016aa,
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+ Author = {{Computational Pan-Genomics Consortium}},
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+ @article{Marcus:2014xy,
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+ Author = {Marcus, Shoshana and Lee, Hayan and Schatz, Michael C},
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+ @article{Baier_2015,
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+ Author = {Baier, Uwe and Beller, Timo and Ohlebusch, Enno},
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+ Journal = {Bioinformatics},
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+ Month = {Oct},
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+ @article{Beller:2016ab,
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+ Author = {Beller, Timo and Ohlebusch, Enno},
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+ @article{Minkin_2016,
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+ Title = {{TwoPaCo}: an efficient algorithm to build the compacted de {Bruijn} graph from many complete genomes},
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+ @article{Chikhi_2016,
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+ Journal = {Bioinformatics},
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+ Month = {Jun},
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+ Doi = {10.1093/bioinformatics/btw279},
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+ Year = {2016}}
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+ @article{Chikhi:2015aa,
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+ Author = {Chikhi, Rayan and Limasset, Antoine and Jackman, Shaun and Simpson, Jared T and Medvedev, Paul},
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+ Journal = {J Comput Biol},
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+ Volume = {22},
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+ Year = {2015}}
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+ @article{Dilthey_2015,
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+ Author = {Dilthey, Alexander and Cox, Charles and Iqbal, Zamin and Nelson, Matthew R and McVean, Gil},
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+ Journal = {Nature Genetics},
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+ Month = {Apr},
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+ Number = {6},
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+ Volume = {47},
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+ Year = {2015}}
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+ @article{Eggertsson:2017aa,
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+ Author = {Eggertsson, Hannes P and Jonsson, Hakon and Kristmundsdottir, Snaedis and Hjartarson, Eirikur and Kehr, Birte and Masson, Gisli and Zink, Florian and Hjorleifsson, Kristjan E and Jonasdottir, Aslaug and Jonasdottir, Adalbjorg and Jonsdottir, Ingileif and Gudbjartsson, Daniel F and Melsted, Pall and Stefansson, Kari and Halldorsson, Bjarni V},
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+ Journal = {Nat Genet},
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+ Month = {Nov},
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+ Pages = {1654-1660},
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+ Volume = {49},
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+ Doi = {10.1038/ng.3964},
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+ Year = {2017}}
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+ @article{Rakocevic_2019,
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+ Author = {Rakocevic, Goran and Semenyuk, Vladimir and Lee, Wan-Ping and Spencer, James and Browning, John and Johnson, Ivan J. and Arsenijevic, Vladan and Nadj, Jelena and Ghose, Kaushik and Suciu, Maria C. and et al.},
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+ Journal = {Nature Genetics},
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+ Month = {Jan},
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+ Number = {2},
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+ Pages = {354--362},
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+ Title = {Fast and accurate genomic analyses using genome graphs},
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+ Year = {2019}}
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+ @article{Garrison:2018aa,
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+ Author = {Garrison, Erik and Sir{\'e}n, Jouni and Novak, Adam M and Hickey, Glenn and Eizenga, Jordan M and Dawson, Eric T and Jones, William and Garg, Shilpa and Markello, Charles and Lin, Michael F and Paten, Benedict and Durbin, Richard},
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+ Journal = {Nat Biotechnol},
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+ Month = {Oct},
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+ Pages = {875-879},
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+ Title = {Variation graph toolkit improves read mapping by representing genetic variation in the reference},
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+ Doi = {10.1038/nbt.4227},
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+ Volume = {36},
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+ Year = {2018}}
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+ @article{Sibbesen:2018aa,
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+ Author = {Sibbesen, Jonas Andreas and Maretty, Lasse and {Danish Pan-Genome Consortium} and Krogh, Anders},
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+ Journal = {Nat Genet},
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+ Month = {Jul},
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+ Pages = {1054-1059},
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+ Title = {Accurate genotyping across variant classes and lengths using variant graphs},
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+ Year = {2018}}
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+ @article{Li:2016aa,
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+ Author = {Li, Heng},
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+ Journal = {Bioinformatics},
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+ Month = {Jul},
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+ Volume = {32},
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+ Year = {2016}}
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+ @article{Rautiainen810812,
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+ Journal = {bioRxiv},
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+ Title = {{GraphAligner}: Rapid and Versatile Sequence-to-Graph Alignment},
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+ year = {2019}}
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+ Year = {2018}}
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+ @article{Ono:2013aa,
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+ Author = {Ono, Yukiteru and Asai, Kiyoshi and Hamada, Michiaki},
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+ Journal = {Bioinformatics},
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+ Year = {2013}}
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+ @article{Garg810341,
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+ Author = {Garg, Shilpa and Fungtammasan, Arkarachai and Carroll, Andrew and Chou, Mike and Schmitt, Anthony and Zhou, Xiang and Mac, Stephen and Peluso, Paul and Hatas, Emily and Ghurye, Jay and Maguire, Jared and Mahmoud, Medhat and Cheng, Haoyu and Heller, David and Zook, Justin M. and Moemke, Tobias and Marschall, Tobias and Sedlazeck, Fritz J. and Aach, John and Chin, Chen-Shan and Church, George M. and Li, Heng},
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+ Journal = {bioRxiv},
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+ Title = {Efficient chromosome-scale haplotype-resolved assembly of human genomes},
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+ Doi = {10.1101/810341},
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+ Year = {2019}}
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+
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+ @article{Robinson:2011aa,
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+ Journal = {Nat Biotechnol},
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+ Month = {Jan},
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+ Doi = {10.1038/nbt.1754},
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+ Year = {2011}}
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+ @article{Mathews:2003aa,
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+ Author = {Mathews, Lauren M and Chi, Susan Y and Greenberg, Noam and Ovchinnikov, Igor and Swergold, Gary D},
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+ Journal = {Am J Hum Genet},
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+ Month = {Mar},
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+ Pages = {739-48},
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+ Title = {Large differences between {LINE-1} amplification rates in the human and chimpanzee lineages},
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+ Volume = {72},
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+ Year = {2003}}
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+ @article{Biederstedt:2018aa,
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+ Author = {Biederstedt, Evan and Oliver, Jeffrey C and Hansen, Nancy F and Jajoo, Aarti and Dunn, Nathan and Olson, Andrew and Busby, Ben and Dilthey, Alexander T},
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+ Journal = {F1000Res},
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+ Pages = {1391},
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+ Title = {{NovoGraph}: Human genome graph construction from multiple long-read de novo assemblies},
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+ Volume = {7},
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+ Doi = {10.12688/f1000research.15895.2},
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+ Year = {2018}}
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+
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+ @inproceedings{DBLP:conf/wabi/AbouelhodaO03,
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+ Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
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