kmer-percolation.bib

% 18349386 
@Article{pmid18349386,
   Author="Zerbino, D. R.  and Birney, E. ",
   Title="{{V}elvet: algorithms for de novo short read assembly using de {B}ruijn graphs}",
   Journal="Genome Res.",
   Year="2008",
   Volume="18",
   Pages="821--829",
   Month="May"
}

@Article{wald43,
   Author="Wald, A",
   Title="Tests of Statistical Hypotheses Concerning Several Parameters When the Number
of Observations is Large",
   Journal="Transactions of the American Mathematical Society",
   Year="1943",
   Volume="54",
   Pages="426-482"
}

% 19251739 
@Article{pmid19251739,
   Author="Simpson, J. T.  and Wong, K.  and Jackman, S. D.  and Schein, J. E.  and Jones, S. J.  and Birol, I. ",
   Title="{{A}{B}y{S}{S}: a parallel assembler for short read sequence data}",
   Journal="Genome Res.",
   Year="2009",
   Volume="19",
   Pages="1117--1123",
   Month="Jun"
}
% 20203603 
@Article{pmid20203603,
   Author="Qin, J.  and Li, R.  and Raes, J.  and Arumugam, M.  and Burgdorf, K. S.  and Manichanh, C.  and Nielsen, T.  and Pons, N.  and Levenez, F.  and Yamada, T.  and Mende, D. R.  and Li, J.  and Xu, J.  and Li, S.  and Li, D.  and Cao, J.  and Wang, B.  and Liang, H.  and Zheng, H.  and Xie, Y.  and Tap, J.  and Lepage, P.  and Bertalan, M.  and Batto, J. M.  and Hansen, T.  and Le Paslier, D.  and Linneberg, A.  and Nielsen, H. B.  and Pelletier, E.  and Renault, P.  and Sicheritz-Ponten, T.  and Turner, K.  and Zhu, H.  and Yu, C.  and Li, S.  and Jian, M.  and Zhou, Y.  and Li, Y.  and Zhang, X.  and Li, S.  and Qin, N.  and Yang, H.  and Wang, J.  and Brunak, S.  and Dore, J.  and Guarner, F.  and Kristiansen, K.  and Pedersen, O.  and Parkhill, J.  and Weissenbach, J.  and Bork, P.  and Ehrlich, S. D.  and Wang, J.  and Antolin, M.  and Artiguenave, F.  and Blottiere, H.  and Borruel, N.  and Bruls, T.  and Casellas, F.  and Chervaux, C.  and Cultrone, A.  and Delorme, C.  and Denariaz, G.  and Dervyn, R.  and Forte, M.  and Friss, C.  and van de Guchte, M.  and Guedon, E.  and Haimet, F.  and Jamet, A.  and Juste, C.  and Kaci, G.  and Kleerebezem, M.  and Knol, J.  and Kristensen, M.  and Layec, S.  and Le Roux, K.  and Leclerc, M.  and Maguin, E.  and Minardi, R. M.  and Oozeer, R.  and Rescigno, M.  and Sanchez, N.  and Tims, S.  and Torrejon, T.  and Varela, E.  and de Vos, W.  and Winogradsky, Y.  and Zoetendal, E. ",
   Title="{{A} human gut microbial gene catalogue established by metagenomic sequencing}",
   Journal="Nature",
   Year="2010",
   Volume="464",
   Pages="59--65",
   Month="Mar"
}
% 21187386 
@Article{pmid21187386,
   Author="Gnerre, S.  and Maccallum, I.  and Przybylski, D.  and Ribeiro, F. J.  and Burton, J. N.  and Walker, B. J.  and Sharpe, T.  and Hall, G.  and Shea, T. P.  and Sykes, S.  and Berlin, A. M.  and Aird, D.  and Costello, M.  and Daza, R.  and Williams, L.  and Nicol, R.  and Gnirke, A.  and Nusbaum, C.  and Lander, E. S.  and Jaffe, D. B. ",
   Title="{{H}igh-quality draft assemblies of mammalian genomes from massively parallel sequence data}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2011",
   Volume="108",
   Pages="1513--1518",
   Month="Jan"
}
% 21273488 
@Article{pmid21273488,
   Author="Hess, M.  and Sczyrba, A.  and Egan, R.  and Kim, T. W.  and Chokhawala, H.  and Schroth, G.  and Luo, S.  and Clark, D. S.  and Chen, F.  and Zhang, T.  and Mackie, R. I.  and Pennacchio, L. A.  and Tringe, S. G.  and Visel, A.  and Woyke, T.  and Wang, Z.  and Rubin, E. M. ",
   Title="{{M}etagenomic discovery of biomass-degrading genes and genomes from cow rumen}",
   Journal="Science",
   Year="2011",
   Volume="331",
   Pages="463--467",
   Month="Jan"
}
% 11504945 
@Article{pmid11504945,
   Author="Pevzner, P. A.  and Tang, H.  and Waterman, M. S. ",
   Title="{{A}n {E}ulerian path approach to {D}{N}{A} fragment assembly}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2001",
   Volume="98",
   Pages="9748--9753",
   Month="Aug"
}
% Bloom filter paper
@Article{bloom,
   Author="Bloom, B. ",
   Title="{{S}pace/time tradeoffs in hash coding with allowable errors}",
   Journal="CACM",
   Year="1970",
   Volume="13(7)",
   Pages="422--426"
}
% 20426693 
@Article{pmid20426693,
   Author="Shi, H.  and Schmidt, B.  and Liu, W.  and Muller-Wittig, W. ",
   Title="{{A} parallel algorithm for error correction in high-throughput short-read data on {C}{U}{D}{A}-enabled graphics hardware}",
   Journal="J. Comput. Biol.",
   Year="2010",
   Volume="17",
   Pages="603--615",
   Month="Apr"
}
% 20472541 
@Article{pmid20472541,
   Author="Stranneheim, H.  and Kaller, M.  and Allander, T.  and Andersson, B.  and Arvestad, L.  and Lundeberg, J. ",
   Title="{{C}lassification of {D}{N}{A} sequences using {B}loom filters}",
   Journal="Bioinformatics",
   Year="2010",
   Volume="26",
   Pages="1595--1600",
   Month="Jul"
}
@incollection {haskell,
   author = {Malde, Ketil and O’Sullivan, Bryan},
   affiliation = {Institute of Marine Research Bergen Norway},
   title = {Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell},
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   editor = {Gill, Andy and Swift, Terrance},
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   isbn = {},
   pages = {183-194},
   volume = {5418},
   year = {2009}
}
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@article{arachne,
  title={ARACHNE: a whole-genome shotgun assembler},
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@article{pcap,
  title={Generating a genome assembly with PCAP},
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  journal={Current Protocols in Bioinformatics},
  year={2005},
  publisher={Wiley Online Library}
}
@article{newbler,
  title={Genome sequencing in open microfabricated high density picoliter reactors},
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@article{adami2002critical,
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@article{hydra,
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@article{bondy2008graph,
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  year={2008}
}
@article{stauffer1979scaling,
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@article{trinity,
  title={{F}ull-length transcriptome assembly from {R}{N}{A}-{S}eq data without a reference genome},
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  year={2011},
  publisher={Nature Publishing Group}
}
@article{panda,
  title={{T}he sequence and de novo assembly of the giant panda genome},
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@article{metavelvet,
  title={{M}eta{V}elvet: {A}n extension of {V}elvet assembler to de novo metagenome assembly from short sequence reads},
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@inproceedings{zhang2003dna,
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}
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@Article{zerbinothesis,
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