error.corr_PeerJ.bbl

\begin{thebibliography}{41}
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%Type = Article
\bibitem[{Auer and Doerge(2011)}]{Auer:2011bt}
\bibinfo{author}{Auer, P.L.}, \bibinfo{author}{Doerge, R.W.},
  \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{A Two-Stage Poisson Model for Testing RNA-Seq
  Data}}.
\newblock \bibinfo{journal}{Statistical Applications in Genetics and Molecular
  Biology} \bibinfo{volume}{10}, \bibinfo{pages}{1--26}.
%Type = Article
\bibitem[{Bradnam et~al.(2013)Bradnam, Fass, Alexandrov, Baranay, Bechner,
  Boisvert10, Chapman, Chapuis, Chikhi, Chitsaz, Chou, Corbeil, Del~Fabbro,
  Docking, Durbin, Earl, Emrich, Fedotov, Fonseca, Ganapathy, Gibbs, Gnerre,
  Godzaridis, Goldstein, Haimel, Hall, Haussler, Hiatt, Ho, Howard, Hunt,
  Jackman, Jaffe, Jarvis, Jiang, Kazakov, Kersey, Kitzman, Knight, Koren, Lam,
  Lavenier, Laviolette, Li, Li, Liu, Liu, Luo, MacCallum, MacManes, Maillet,
  Melnikov, Vieira, Naquin, Ning, Otto, Paten, Paulo, Phillippy, Pina-Martins,
  Place, Przybylski, Qin, Qu, Ribeiro, Richards, Rokhsar, Ruby, Scalabrin,
  Schatz, Schwartz, Sergushichev, Sharpe, Shaw, Shendure, Shi, Simpson, Song,
  Tsarev, Vezzi, Vicedomini, Wang, Worley, Yin, Yiu, Yuan, Zhang, Zhang, Zhou
  and Korf}]{Bradnam:2013uu}
\bibinfo{author}{Bradnam, K.R.}, \bibinfo{author}{Fass, J.N.},
  \bibinfo{author}{Alexandrov, A.}, \bibinfo{author}{Baranay, P.},
  \bibinfo{author}{Bechner, M.}, \bibinfo{author}{Boisvert10, S.},
  \bibinfo{author}{Chapman, J.A.}, \bibinfo{author}{Chapuis, G.},
  \bibinfo{author}{Chikhi, R.}, \bibinfo{author}{Chitsaz, H.},
  \bibinfo{author}{Chou, W.C.}, \bibinfo{author}{Corbeil, J.},
  \bibinfo{author}{Del~Fabbro, C.}, \bibinfo{author}{Docking, T.R.},
  \bibinfo{author}{Durbin, R.}, \bibinfo{author}{Earl, D.},
  \bibinfo{author}{Emrich, S.}, \bibinfo{author}{Fedotov, P.},
  \bibinfo{author}{Fonseca, N.A.}, \bibinfo{author}{Ganapathy, G.},
  \bibinfo{author}{Gibbs, R.A.}, \bibinfo{author}{Gnerre, S.},
  \bibinfo{author}{Godzaridis, {\'E}.}, \bibinfo{author}{Goldstein, S.},
  \bibinfo{author}{Haimel, M.}, \bibinfo{author}{Hall, G.},
  \bibinfo{author}{Haussler, D.}, \bibinfo{author}{Hiatt, J.B.},
  \bibinfo{author}{Ho, I.Y.}, \bibinfo{author}{Howard, J.},
  \bibinfo{author}{Hunt, M.}, \bibinfo{author}{Jackman, S.D.},
  \bibinfo{author}{Jaffe, D.B.}, \bibinfo{author}{Jarvis, E.},
  \bibinfo{author}{Jiang, H.}, \bibinfo{author}{Kazakov, S.},
  \bibinfo{author}{Kersey, P.J.}, \bibinfo{author}{Kitzman, J.O.},
  \bibinfo{author}{Knight, J.R.}, \bibinfo{author}{Koren, S.},
  \bibinfo{author}{Lam, T.W.}, \bibinfo{author}{Lavenier, D.},
  \bibinfo{author}{Laviolette, F.}, \bibinfo{author}{Li, Y.},
  \bibinfo{author}{Li, Z.}, \bibinfo{author}{Liu, B.}, \bibinfo{author}{Liu,
  Y.}, \bibinfo{author}{Luo, R.}, \bibinfo{author}{MacCallum, I.},
  \bibinfo{author}{MacManes, M.D.}, \bibinfo{author}{Maillet, N.},
  \bibinfo{author}{Melnikov, S.}, \bibinfo{author}{Vieira, B.M.},
  \bibinfo{author}{Naquin, D.}, \bibinfo{author}{Ning, Z.},
  \bibinfo{author}{Otto, T.D.}, \bibinfo{author}{Paten, B.},
  \bibinfo{author}{Paulo, O.S.}, \bibinfo{author}{Phillippy, A.M.},
  \bibinfo{author}{Pina-Martins, F.}, \bibinfo{author}{Place, M.},
  \bibinfo{author}{Przybylski, D.}, \bibinfo{author}{Qin, X.},
  \bibinfo{author}{Qu, C.}, \bibinfo{author}{Ribeiro, F.J.},
  \bibinfo{author}{Richards, S.}, \bibinfo{author}{Rokhsar, D.S.},
  \bibinfo{author}{Ruby, J.G.}, \bibinfo{author}{Scalabrin, S.},
  \bibinfo{author}{Schatz, M.C.}, \bibinfo{author}{Schwartz, D.C.},
  \bibinfo{author}{Sergushichev, A.}, \bibinfo{author}{Sharpe, T.},
  \bibinfo{author}{Shaw, T.I.}, \bibinfo{author}{Shendure, J.},
  \bibinfo{author}{Shi, Y.}, \bibinfo{author}{Simpson, J.T.},
  \bibinfo{author}{Song, H.}, \bibinfo{author}{Tsarev, F.},
  \bibinfo{author}{Vezzi, F.}, \bibinfo{author}{Vicedomini, R.},
  \bibinfo{author}{Wang, J.}, \bibinfo{author}{Worley, K.C.},
  \bibinfo{author}{Yin, S.}, \bibinfo{author}{Yiu, S.M.},
  \bibinfo{author}{Yuan, J.}, \bibinfo{author}{Zhang, G.},
  \bibinfo{author}{Zhang, H.}, \bibinfo{author}{Zhou, S.},
  \bibinfo{author}{Korf, I.F.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{Assemblathon 2: evaluating \textit{de novo} methods
  of genome assembly in three vertebrate species}}.
\newblock \bibinfo{journal}{arXiv.org}
  \href{http://arxiv.org/abs/1301.5406v1}{\tt arXiv:1301.5406v1}.
%Type = Article
\bibitem[{Camacho et~al.(2009)Camacho, Coulouris, Avagyan, Ma, Papadopoulos,
  Bealer and Madden}]{Camacho:2009fc}
\bibinfo{author}{Camacho, C.}, \bibinfo{author}{Coulouris, G.},
  \bibinfo{author}{Avagyan, V.}, \bibinfo{author}{Ma, N.},
  \bibinfo{author}{Papadopoulos, J.}, \bibinfo{author}{Bealer, K.},
  \bibinfo{author}{Madden, T.L.}, \bibinfo{year}{2009}.
\newblock \bibinfo{title}{{BLAST+: architecture and applications}}.
\newblock \bibinfo{journal}{BMC Bioinformatics} \bibinfo{volume}{10},
  \bibinfo{pages}{421}.
%Type = Article
\bibitem[{Chaisson et~al.(2004)Chaisson, Pevzner and Tang}]{Chaisson:2004kf}
\bibinfo{author}{Chaisson, M.}, \bibinfo{author}{Pevzner, P.},
  \bibinfo{author}{Tang, H.X.}, \bibinfo{year}{2004}.
\newblock \bibinfo{title}{{Fragment assembly with short reads}}.
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{20}, \bibinfo{pages}{2067--2074}.
%Type = Article
\bibitem[{Chen et~al.(2011)Chen, Liu, Ng, Nadarajah, Kaufman, Yang and
  Deng}]{Chen:2011ba}
\bibinfo{author}{Chen, Z.}, \bibinfo{author}{Liu, J.}, \bibinfo{author}{Ng,
  H.K.T.}, \bibinfo{author}{Nadarajah, S.}, \bibinfo{author}{Kaufman, H.L.},
  \bibinfo{author}{Yang, J.Y.}, \bibinfo{author}{Deng, Y.},
  \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Statistical methods on detecting differentially
  expressed genes for RNA-seq data}}.
\newblock \bibinfo{journal}{BMC Systems Biology} \bibinfo{volume}{5},
  \bibinfo{pages}{S1}.
%Type = Article
\bibitem[{Conway and Bromage(2011)}]{Conway:2011iv}
\bibinfo{author}{Conway, T.C.}, \bibinfo{author}{Bromage, a.J.},
  \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Succinct data structures for assembling large
  genomes.}}
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{27}, \bibinfo{pages}{479--486}.
%Type = Article
\bibitem[{Cox et~al.(2010)Cox, Peterson and Biggs}]{Cox:2010ch}
\bibinfo{author}{Cox, M.P.}, \bibinfo{author}{Peterson, D.A.},
  \bibinfo{author}{Biggs, P.J.}, \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{SolexaQA: At-a-glance quality assessment of Illumina
  second-generation sequencing data}}.
\newblock \bibinfo{journal}{BMC Bioinformatics} \bibinfo{volume}{11},
  \bibinfo{pages}{485}.
%Type = Article
\bibitem[{Earl et~al.(2011)Earl, Bradnam, St~John, Darling, Lin, Fass, Yu,
  Buffalo, Zerbino, Diekhans, Nguyen, Ariyaratne, Sung, Ning, Haimel, Simpson,
  Fonseca, Birol, Docking, Ho, Rokhsar, Chikhi, Lavenier, Chapuis, Naquin,
  Maillet, Schatz, Kelley, Phillippy, Koren, Yang, Wu, Chou, Srivastava, Shaw,
  Ruby, Skewes-Cox, Betegon, Dimon, Solovyev, Seledtsov, Kosarev, Vorobyev,
  Ramirez-Gonzalez, Leggett, MacLean, Xia, Luo, Li, Xie, Liu, Gnerre,
  Maccallum, Przybylski, Ribeiro, Yin, Sharpe, Hall, Kersey, Durbin, Jackman,
  Chapman, Huang, DeRisi, Caccamo, Li, Jaffe, Green, Haussler, Korf and
  Paten}]{Earl:2011gt}
\bibinfo{author}{Earl, D.}, \bibinfo{author}{Bradnam, K.},
  \bibinfo{author}{St~John, J.}, \bibinfo{author}{Darling, A.},
  \bibinfo{author}{Lin, D.}, \bibinfo{author}{Fass, J.}, \bibinfo{author}{Yu,
  H.O.K.}, \bibinfo{author}{Buffalo, V.}, \bibinfo{author}{Zerbino, D.R.},
  \bibinfo{author}{Diekhans, M.}, \bibinfo{author}{Nguyen, N.},
  \bibinfo{author}{Ariyaratne, P.N.}, \bibinfo{author}{Sung, W.K.},
  \bibinfo{author}{Ning, Z.}, \bibinfo{author}{Haimel, M.},
  \bibinfo{author}{Simpson, J.T.}, \bibinfo{author}{Fonseca, N.A.},
  \bibinfo{author}{Birol, I.}, \bibinfo{author}{Docking, T.R.},
  \bibinfo{author}{Ho, I.Y.}, \bibinfo{author}{Rokhsar, D.S.},
  \bibinfo{author}{Chikhi, R.}, \bibinfo{author}{Lavenier, D.},
  \bibinfo{author}{Chapuis, G.}, \bibinfo{author}{Naquin, D.},
  \bibinfo{author}{Maillet, N.}, \bibinfo{author}{Schatz, M.C.},
  \bibinfo{author}{Kelley, D.R.}, \bibinfo{author}{Phillippy, A.M.},
  \bibinfo{author}{Koren, S.}, \bibinfo{author}{Yang, S.P.},
  \bibinfo{author}{Wu, W.}, \bibinfo{author}{Chou, W.C.},
  \bibinfo{author}{Srivastava, A.}, \bibinfo{author}{Shaw, T.I.},
  \bibinfo{author}{Ruby, J.G.}, \bibinfo{author}{Skewes-Cox, P.},
  \bibinfo{author}{Betegon, M.}, \bibinfo{author}{Dimon, M.T.},
  \bibinfo{author}{Solovyev, V.}, \bibinfo{author}{Seledtsov, I.},
  \bibinfo{author}{Kosarev, P.}, \bibinfo{author}{Vorobyev, D.},
  \bibinfo{author}{Ramirez-Gonzalez, R.}, \bibinfo{author}{Leggett, R.},
  \bibinfo{author}{MacLean, D.}, \bibinfo{author}{Xia, F.},
  \bibinfo{author}{Luo, R.}, \bibinfo{author}{Li, Z.}, \bibinfo{author}{Xie,
  Y.}, \bibinfo{author}{Liu, B.}, \bibinfo{author}{Gnerre, S.},
  \bibinfo{author}{Maccallum, I.}, \bibinfo{author}{Przybylski, D.},
  \bibinfo{author}{Ribeiro, F.J.}, \bibinfo{author}{Yin, S.},
  \bibinfo{author}{Sharpe, T.}, \bibinfo{author}{Hall, G.},
  \bibinfo{author}{Kersey, P.J.}, \bibinfo{author}{Durbin, R.},
  \bibinfo{author}{Jackman, S.D.}, \bibinfo{author}{Chapman, J.A.},
  \bibinfo{author}{Huang, X.}, \bibinfo{author}{DeRisi, J.L.},
  \bibinfo{author}{Caccamo, M.}, \bibinfo{author}{Li, Y.},
  \bibinfo{author}{Jaffe, D.B.}, \bibinfo{author}{Green, R.E.},
  \bibinfo{author}{Haussler, D.}, \bibinfo{author}{Korf, I.},
  \bibinfo{author}{Paten, B.}, \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Assemblathon 1: A competitive assessment of
  \textit{de novo} short read assembly methods}}.
\newblock \bibinfo{journal}{Genome Research} \bibinfo{volume}{21},
  \bibinfo{pages}{2224--2241}.
%Type = Article
\bibitem[{Francis et~al.(2013)Francis, Christianson, Kiko, Powers, Shaner and
  Haddock}]{Francis:2013gc}
\bibinfo{author}{Francis, W.R.}, \bibinfo{author}{Christianson, L.M.},
  \bibinfo{author}{Kiko, R.}, \bibinfo{author}{Powers, M.L.},
  \bibinfo{author}{Shaner, N.C.}, \bibinfo{author}{Haddock, S.H.D.},
  \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{A comparison across non-model animals suggests an
  optimal sequencing depth for \textit{de novo} transcriptome assembly}}.
\newblock \bibinfo{journal}{BMC Genomics} \bibinfo{volume}{14},
  \bibinfo{pages}{167}.
%Type = Article
\bibitem[{Gnerre et~al.(2011)Gnerre, MacCallum, Przybylski, Ribeiro, Burton,
  Walker, Sharpe, Hall, Shea, Sykes, Berlin, Aird, Costello, Daza, Williams,
  Nicol, Gnirke, Nusbaum, Lander and Jaffe}]{Gnerre:2011fd}
\bibinfo{author}{Gnerre, S.}, \bibinfo{author}{MacCallum, I.},
  \bibinfo{author}{Przybylski, D.}, \bibinfo{author}{Ribeiro, F.J.},
  \bibinfo{author}{Burton, J.N.}, \bibinfo{author}{Walker, B.J.},
  \bibinfo{author}{Sharpe, T.}, \bibinfo{author}{Hall, G.},
  \bibinfo{author}{Shea, T.P.}, \bibinfo{author}{Sykes, S.},
  \bibinfo{author}{Berlin, A.M.}, \bibinfo{author}{Aird, D.},
  \bibinfo{author}{Costello, M.}, \bibinfo{author}{Daza, R.},
  \bibinfo{author}{Williams, L.}, \bibinfo{author}{Nicol, R.},
  \bibinfo{author}{Gnirke, a.}, \bibinfo{author}{Nusbaum, C.},
  \bibinfo{author}{Lander, E.S.}, \bibinfo{author}{Jaffe, D.B.},
  \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{High-quality draft assemblies of mammalian genomes
  from massively parallel sequence data.}}
\newblock \bibinfo{journal}{Proceedings of the National Academy of Sciences}
  \bibinfo{volume}{108}, \bibinfo{pages}{1513--1518}.
%Type = Article
\bibitem[{Grabherr et~al.(2011)Grabherr, Haas, Yassour, Levin, Thompson, Amit,
  Adiconis, Fan, Raychowdhury, Zeng, Chen, Mauceli, Hacohen, Gnirke, Rhind,
  di~Palma, Birren, Nusbaum, Lindblad-Toh, Friedman and
  Regev}]{Grabherr:2011jb}
\bibinfo{author}{Grabherr, M.G.}, \bibinfo{author}{Haas, B.J.},
  \bibinfo{author}{Yassour, M.}, \bibinfo{author}{Levin, J.Z.},
  \bibinfo{author}{Thompson, D.A.}, \bibinfo{author}{Amit, I.},
  \bibinfo{author}{Adiconis, X.}, \bibinfo{author}{Fan, L.},
  \bibinfo{author}{Raychowdhury, R.}, \bibinfo{author}{Zeng, Q.},
  \bibinfo{author}{Chen, Z.}, \bibinfo{author}{Mauceli, E.},
  \bibinfo{author}{Hacohen, N.}, \bibinfo{author}{Gnirke, a.},
  \bibinfo{author}{Rhind, N.}, \bibinfo{author}{di~Palma, F.},
  \bibinfo{author}{Birren, B.W.}, \bibinfo{author}{Nusbaum, C.},
  \bibinfo{author}{Lindblad-Toh, K.}, \bibinfo{author}{Friedman, N.},
  \bibinfo{author}{Regev, A.}, \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Full-length transcriptome assembly from RNA-Seq data
  without a reference genome.}}
\newblock \bibinfo{journal}{Nature Biotechnology} \bibinfo{volume}{29},
  \bibinfo{pages}{644--652}.
%Type = Article
\bibitem[{Griebel et~al.(2012)Griebel, Zacher, Ribeca, Raineri, Lacroix,
  Guig{\'o} and Sammeth}]{Griebel:2012ti}
\bibinfo{author}{Griebel, T.}, \bibinfo{author}{Zacher, B.},
  \bibinfo{author}{Ribeca, P.}, \bibinfo{author}{Raineri, E.},
  \bibinfo{author}{Lacroix, V.}, \bibinfo{author}{Guig{\'o}, R.},
  \bibinfo{author}{Sammeth, M.}, \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{Modelling and simulating generic RNA-Seq experiments
  with the flux simulator.}}
\newblock \bibinfo{journal}{Nucleic Acids Research} \bibinfo{volume}{40},
  \bibinfo{pages}{10073--10083}.
%Type = Article
\bibitem[{Haas et~al.(2013)Haas, Papanicolaou, Yassour, Grabherr, Blood,
  Bowden, Couger, Eccles, Li, Lieber, MacManes, Ott, Orvis, Pochet, Strozzi,
  Weeks, Westerman, William, Dewey, Henschel, LeDuc, Friedman and
  Regev}]{Haas:jq}
\bibinfo{author}{Haas, B.J.}, \bibinfo{author}{Papanicolaou, A.},
  \bibinfo{author}{Yassour, M.}, \bibinfo{author}{Grabherr, M.},
  \bibinfo{author}{Blood, P.}, \bibinfo{author}{Bowden, J.},
  \bibinfo{author}{Couger, M.}, \bibinfo{author}{Eccles, D.},
  \bibinfo{author}{Li, B.}, \bibinfo{author}{Lieber, M.},
  \bibinfo{author}{MacManes, M.D.}, \bibinfo{author}{Ott, M.},
  \bibinfo{author}{Orvis, J.}, \bibinfo{author}{Pochet, N.},
  \bibinfo{author}{Strozzi, F.}, \bibinfo{author}{Weeks, N.},
  \bibinfo{author}{Westerman, R.}, \bibinfo{author}{William, T.},
  \bibinfo{author}{Dewey, C.N.}, \bibinfo{author}{Henschel, R.},
  \bibinfo{author}{LeDuc, R.G.}, \bibinfo{author}{Friedman, N.},
  \bibinfo{author}{Regev, A.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{\emph{\textit{De novo}} transcript sequence
  reconstruction from RNA-seq using the Trinity platform for reference
  generation and analysis}}.
\newblock \bibinfo{journal}{Nature protocols} , \bibinfo{pages}{1--21}.
%Type = Article
\bibitem[{Hsu et~al.(2012)Hsu, Chien, Hu, Chen, Wu, Feng, Haymer and
  Chen}]{Hsu:2012dg}
\bibinfo{author}{Hsu, J.C.}, \bibinfo{author}{Chien, T.Y.},
  \bibinfo{author}{Hu, C.C.}, \bibinfo{author}{Chen, M.J.M.},
  \bibinfo{author}{Wu, W.J.}, \bibinfo{author}{Feng, H.T.},
  \bibinfo{author}{Haymer, D.S.}, \bibinfo{author}{Chen, C.Y.},
  \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{Discovery of Genes Related to Insecticide Resistance
  in \emph{Bactrocera dorsalis} by Functional Genomic Analysis of a \emph{De
  Novo} Assembled Transcriptome}}.
\newblock \bibinfo{journal}{PLOS ONE} \bibinfo{volume}{7},
  \bibinfo{pages}{e40950}.
%Type = Article
\bibitem[{Hu et~al.(2011)Hu, Zhu, Taylor, Liu and Qin}]{Hu:2011cn}
\bibinfo{author}{Hu, M.}, \bibinfo{author}{Zhu, Y.}, \bibinfo{author}{Taylor,
  J.M.G.}, \bibinfo{author}{Liu, J.S.}, \bibinfo{author}{Qin, Z.S.},
  \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Using Poisson mixed-effects model to quantify
  transcript-level gene expression in RNA-Seq}}.
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{28}, \bibinfo{pages}{63--68}.
%Type = Article
\bibitem[{Jiang and Wong(2009)}]{Jiang:2009bw}
\bibinfo{author}{Jiang, H.}, \bibinfo{author}{Wong, W.H.},
  \bibinfo{year}{2009}.
\newblock \bibinfo{title}{{Statistical inferences for isoform expression in
  RNA-Seq}}.
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{25}, \bibinfo{pages}{1026--1032}.
%Type = Article
\bibitem[{Kao et~al.(2011)Kao, Chan and Song}]{Kao:2011bx}
\bibinfo{author}{Kao, W.C.}, \bibinfo{author}{Chan, a.H.},
  \bibinfo{author}{Song, Y.S.}, \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{ECHO: a reference-free short-read error correction
  algorithm.}}
\newblock \bibinfo{journal}{Genome Research} \bibinfo{volume}{21},
  \bibinfo{pages}{1181--1192}.
%Type = Article
\bibitem[{Kelley et~al.(2010)Kelley, Schatz and Salzberg}]{Kelley:2010kg}
\bibinfo{author}{Kelley, D.R.}, \bibinfo{author}{Schatz, M.C.},
  \bibinfo{author}{Salzberg, S.L.}, \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{Quake: quality-aware detection and correction of
  sequencing errors}}.
\newblock \bibinfo{journal}{Genome Biology} \bibinfo{volume}{11},
  \bibinfo{pages}{R116}.
%Type = Article
\bibitem[{Kent(2002)}]{Kent:2002jd}
\bibinfo{author}{Kent, W.J.}, \bibinfo{year}{2002}.
\newblock \bibinfo{title}{{BLAT---The BLAST-Like Alignment Tool}}.
\newblock \bibinfo{journal}{Genome Research} \bibinfo{volume}{12},
  \bibinfo{pages}{656--664}.
%Type = Article
\bibitem[{Le et~al.(2013)Le, Schulz, McCauley, Hinman and
  Bar-Joseph}]{Le:2013dy}
\bibinfo{author}{Le, H.S.}, \bibinfo{author}{Schulz, M.H.},
  \bibinfo{author}{McCauley, B.M.}, \bibinfo{author}{Hinman, V.F.},
  \bibinfo{author}{Bar-Joseph, Z.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{Probabilistic error correction for RNA sequencing}}.
\newblock \bibinfo{journal}{Nucleic Acids Research} .
%Type = Article
\bibitem[{Linnen et~al.(2013)Linnen, Poh, Peterson, Barrett, Larson, Jensen and
  Hoekstra}]{Linnen:2013ir}
\bibinfo{author}{Linnen, C.R.}, \bibinfo{author}{Poh, Y.P.},
  \bibinfo{author}{Peterson, B.K.}, \bibinfo{author}{Barrett, R.D.H.},
  \bibinfo{author}{Larson, J.G.}, \bibinfo{author}{Jensen, J.D.},
  \bibinfo{author}{Hoekstra, H.E.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{Adaptive Evolution of Multiple Traits Through
  Multiple Mutations at a Single Gene}}.
\newblock \bibinfo{journal}{Science (New York, NY)} \bibinfo{volume}{339},
  \bibinfo{pages}{1312--1316}.
%Type = Article
\bibitem[{Liu et~al.(2012)Liu, Yuan, Yiu, Li, Xie, Chen, Shi, Zhang, Li, Lam
  and Luo}]{Liu:2012iv}
\bibinfo{author}{Liu, B.}, \bibinfo{author}{Yuan, J.}, \bibinfo{author}{Yiu,
  S.M.}, \bibinfo{author}{Li, Z.}, \bibinfo{author}{Xie, Y.},
  \bibinfo{author}{Chen, Y.}, \bibinfo{author}{Shi, Y.},
  \bibinfo{author}{Zhang, H.}, \bibinfo{author}{Li, Y.}, \bibinfo{author}{Lam,
  T.W.}, \bibinfo{author}{Luo, R.}, \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{COPE: an accurate k-mer-based pair-end reads
  connection tool to facilitate genome assembly}}.
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{28}, \bibinfo{pages}{2870--2874}.
%Type = Article
\bibitem[{Liu et~al.(2011)Liu, Schmidt and Maskell}]{Liu:2011ez}
\bibinfo{author}{Liu, Y.}, \bibinfo{author}{Schmidt, B.},
  \bibinfo{author}{Maskell, D.L.}, \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{Parallelized short read assembly of large genomes
  using \textit{de Bruijn} graphs.}}
\newblock \bibinfo{journal}{BMC Bioinformatics} \bibinfo{volume}{12},
  \bibinfo{pages}{354}.
%Type = Article
\bibitem[{Maccallum et~al.(2009)Maccallum, Przybylski, Gnerre, Burton,
  Shlyakhter, Gnirke, Malek, McKernan, Ranade, Shea, Williams, Young, Nusbaum
  and Jaffe}]{Maccallum:2009du}
\bibinfo{author}{Maccallum, I.}, \bibinfo{author}{Przybylski, D.},
  \bibinfo{author}{Gnerre, S.}, \bibinfo{author}{Burton, J.},
  \bibinfo{author}{Shlyakhter, I.}, \bibinfo{author}{Gnirke, A.},
  \bibinfo{author}{Malek, J.}, \bibinfo{author}{McKernan, K.},
  \bibinfo{author}{Ranade, S.}, \bibinfo{author}{Shea, T.},
  \bibinfo{author}{Williams, L.}, \bibinfo{author}{Young, S.},
  \bibinfo{author}{Nusbaum, C.}, \bibinfo{author}{Jaffe, D.},
  \bibinfo{year}{2009}.
\newblock \bibinfo{title}{{ALLPATHS 2: small genomes assembled accurately and
  with high continuity from short paired reads}}.
\newblock \bibinfo{journal}{Genome Biology} \bibinfo{volume}{10},
  \bibinfo{pages}{R103}.
%Type = Article
\bibitem[{MacManes and Lacey(2012)}]{MacManes:2012bu}
\bibinfo{author}{MacManes, M.D.}, \bibinfo{author}{Lacey, E.A.},
  \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{The Social Brain: Transcriptome Assembly and
  Characterization of the Hippocampus from a Social Subterranean Rodent, the
  Colonial Tuco-Tuco (\textit{Ctenomys} \textit{sociabilis})}}.
\newblock \bibinfo{journal}{PLOS ONE} \bibinfo{volume}{7},
  \bibinfo{pages}{e45524}.
%Type = Article
\bibitem[{Marioni et~al.(2008)Marioni, Mason, Mane, Stephens and
  Gilad}]{Marioni:2008bg}
\bibinfo{author}{Marioni, J.C.}, \bibinfo{author}{Mason, C.E.},
  \bibinfo{author}{Mane, S.M.}, \bibinfo{author}{Stephens, M.},
  \bibinfo{author}{Gilad, Y.}, \bibinfo{year}{2008}.
\newblock \bibinfo{title}{{RNA-seq: An assessment of technical reproducibility
  and comparison with gene expression arrays}}.
\newblock \bibinfo{journal}{Genome Research} \bibinfo{volume}{18},
  \bibinfo{pages}{1509--1517}.
%Type = Article
\bibitem[{Mu\~noz Merida et~al.(2013)Mu\~noz Merida, Gonzalez-Plaza, Canada,
  Blanco, Garcia-Lopez, Rodriguez, Pedrola, Sicardo, Hernandez, De~la Rosa,
  Belaj, Gil-Borja, Luque, Martinez-Rivas, Pisano, Trelles, Valpuesta and
  Beuzon}]{MunozMerida:2013dw}
\bibinfo{author}{Mu\~noz Merida, A.}, \bibinfo{author}{Gonzalez-Plaza, J.J.},
  \bibinfo{author}{Canada, A.}, \bibinfo{author}{Blanco, A.M.},
  \bibinfo{author}{Garcia-Lopez, M.d.C.}, \bibinfo{author}{Rodriguez, J.M.},
  \bibinfo{author}{Pedrola, L.}, \bibinfo{author}{Sicardo, M.D.},
  \bibinfo{author}{Hernandez, M.L.}, \bibinfo{author}{De~la Rosa, R.},
  \bibinfo{author}{Belaj, A.}, \bibinfo{author}{Gil-Borja, M.},
  \bibinfo{author}{Luque, F.}, \bibinfo{author}{Martinez-Rivas, J.M.},
  \bibinfo{author}{Pisano, D.G.}, \bibinfo{author}{Trelles, O.},
  \bibinfo{author}{Valpuesta, V.}, \bibinfo{author}{Beuzon, C.R.},
  \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{De Novo Assembly and Functional Annotation of the
  Olive (\textit{Olea europaea}) Transcriptome}}.
\newblock \bibinfo{journal}{DNA Research} \bibinfo{volume}{20},
  \bibinfo{pages}{93--108}.
%Type = Article
\bibitem[{Miller et~al.(2010)Miller, Koren and Sutton}]{Miller:2010gxa}
\bibinfo{author}{Miller, J.R.}, \bibinfo{author}{Koren, S.},
  \bibinfo{author}{Sutton, G.}, \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{Assembly algorithms for next-generation sequencing
  data}}.
\newblock \bibinfo{journal}{Genomics} \bibinfo{volume}{95},
  \bibinfo{pages}{315--327}.
%Type = Article
\bibitem[{Mortazavi et~al.(2008)Mortazavi, Williams, Mccue, Schaeffer and
  Wold}]{Mortazavi:2008jj}
\bibinfo{author}{Mortazavi, A.}, \bibinfo{author}{Williams, B.A.},
  \bibinfo{author}{Mccue, K.}, \bibinfo{author}{Schaeffer, L.},
  \bibinfo{author}{Wold, B.}, \bibinfo{year}{2008}.
\newblock \bibinfo{title}{{Mapping and quantifying mammalian transcriptomes by
  RNA-Seq}}.
\newblock \bibinfo{journal}{Nature Methods} \bibinfo{volume}{5},
  \bibinfo{pages}{621--628}.
%Type = Article
\bibitem[{Narum et~al.(2013)Narum, Campbell, Meyer, Miller and
  Hardy}]{Narum:2013kc}
\bibinfo{author}{Narum, S.R.}, \bibinfo{author}{Campbell, N.R.},
  \bibinfo{author}{Meyer, K.A.}, \bibinfo{author}{Miller, M.R.},
  \bibinfo{author}{Hardy, R.W.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{Thermal adaptation and acclimation of ectotherms
  from differing aquatic climates.}}
\newblock \bibinfo{journal}{Molecular Ecology} , \bibinfo{pages}{1--8}.
%Type = Article
\bibitem[{Pell et~al.(2012)Pell, Hintze, Canino-Koning, Howe, Tiedje and
  Brown}]{Pell:2012id}
\bibinfo{author}{Pell, J.}, \bibinfo{author}{Hintze, A.},
  \bibinfo{author}{Canino-Koning, R.}, \bibinfo{author}{Howe, A.},
  \bibinfo{author}{Tiedje, J.M.}, \bibinfo{author}{Brown, C.T.},
  \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{Scaling metagenome sequence assembly with
  probabilistic \textit{de Bruijn} graphs.}}
\newblock \bibinfo{journal}{Proceedings of the National Academy of Sciences}
  \bibinfo{volume}{109}, \bibinfo{pages}{13272--13277}.
%Type = Article
\bibitem[{Pyrkosz et~al.(2013)Pyrkosz, Cheng and Brown}]{Pyrkosz:2013tm}
\bibinfo{author}{Pyrkosz, A.B.}, \bibinfo{author}{Cheng, H.},
  \bibinfo{author}{Brown, C.T.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{RNA-Seq Mapping Errors When Using Incomplete
  Reference Transcriptomes of Vertebrates}}.
\newblock \bibinfo{journal}{\url{http://arxiv.org/abs/1303.2411v1}}
  \href{http://arxiv.org/abs/1303.2411v1}{\tt arXiv:1303.2411v1}.
%Type = Article
\bibitem[{R~Core Development~Team(2011)}]{RALanguageandEn:wf}
\bibinfo{author}{R~Core Development~Team, F.}, \bibinfo{year}{2011}.
\newblock \bibinfo{title}{{R: A Language and Environment for Statistical
  Computing}} .
%Type = Article
\bibitem[{Roberts and Pachter(2012)}]{Roberts:2012dh}
\bibinfo{author}{Roberts, A.}, \bibinfo{author}{Pachter, L.},
  \bibinfo{year}{2012}.
\newblock \bibinfo{title}{{Streaming fragment assignment for real-time analysis
  of sequencing experiments}}.
\newblock \bibinfo{journal}{Nature Methods} , \bibinfo{pages}{1--7}.
%Type = Article
\bibitem[{Sammeth(2009)}]{Sammeth:2009jx}
\bibinfo{author}{Sammeth, M.}, \bibinfo{year}{2009}.
\newblock \bibinfo{title}{{Complete alternative splicing events are bubbles in
  splicing graphs.}}
\newblock \bibinfo{journal}{Journal of computational biology : a journal of
  computational molecular cell biology} \bibinfo{volume}{16},
  \bibinfo{pages}{1117--1140}.
%Type = Article
\bibitem[{Simpson and Durbin(2010)}]{Simpson:2010fd}
\bibinfo{author}{Simpson, J.T.}, \bibinfo{author}{Durbin, R.},
  \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{Efficient construction of an assembly string graph
  using the FM-index}}.
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{26}, \bibinfo{pages}{i367--i373}.
%Type = Article
\bibitem[{Soneson and Delorenzi(2013)}]{Soneson:2013fr}
\bibinfo{author}{Soneson, C.}, \bibinfo{author}{Delorenzi, M.},
  \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{A comparison of methods for differential expression
  analysis of RNA-seq data}}.
\newblock \bibinfo{journal}{BMC Bioinformatics} \bibinfo{volume}{14},
  \bibinfo{pages}{91}.
%Type = Article
\bibitem[{Trapnell et~al.(2010)Trapnell, Williams, Pertea, Mortazavi, Kwan, van
  Baren, Salzberg, Wold and Pachter}]{Trapnell:2010kd}
\bibinfo{author}{Trapnell, C.}, \bibinfo{author}{Williams, B.A.},
  \bibinfo{author}{Pertea, G.}, \bibinfo{author}{Mortazavi, A.},
  \bibinfo{author}{Kwan, G.}, \bibinfo{author}{van Baren, M.J.},
  \bibinfo{author}{Salzberg, S.L.}, \bibinfo{author}{Wold, B.J.},
  \bibinfo{author}{Pachter, L.}, \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{Transcript assembly and quantification by RNA-Seq
  reveals unannotated transcripts and isoform switching during cell
  differentiation}}.
\newblock \bibinfo{journal}{Nature Biotechnology} \bibinfo{volume}{28},
  \bibinfo{pages}{511--U174}.
%Type = Article
\bibitem[{Vijay et~al.(2013)Vijay, Poelstra, K{\"u}nstner and
  Wolf}]{Vijay:2012gy}
\bibinfo{author}{Vijay, N.}, \bibinfo{author}{Poelstra, J.W.},
  \bibinfo{author}{K{\"u}nstner, A.}, \bibinfo{author}{Wolf, J.B.W.},
  \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{Challenges and strategies in transcriptome assembly
  and differential gene expression quantification. A comprehensive \textit{in
  silico} assessment of RNA-seq experiments.}}
\newblock \bibinfo{journal}{Molecular Ecology} \bibinfo{volume}{22},
  \bibinfo{pages}{620--634}.
%Type = Article
\bibitem[{Yang et~al.(2013)Yang, Chockalingam and Aluru}]{Yang:2013ck}
\bibinfo{author}{Yang, X.}, \bibinfo{author}{Chockalingam, S.P.},
  \bibinfo{author}{Aluru, S.}, \bibinfo{year}{2013}.
\newblock \bibinfo{title}{{A survey of error-correction methods for
  next-generation sequencing}}.
\newblock \bibinfo{journal}{Briefings In Bioinformatics} \bibinfo{volume}{14},
  \bibinfo{pages}{56--66}.
%Type = Article
\bibitem[{Yang et~al.(2010)Yang, Dorman and Aluru}]{Yang:2010kv}
\bibinfo{author}{Yang, X.}, \bibinfo{author}{Dorman, K.S.},
  \bibinfo{author}{Aluru, S.}, \bibinfo{year}{2010}.
\newblock \bibinfo{title}{{Reptile: representative tiling for short read error
  correction.}}
\newblock \bibinfo{journal}{Bioinformatics (Oxford, England)}
  \bibinfo{volume}{26}, \bibinfo{pages}{2526--2533}.

\end{thebibliography}