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another set of fixes

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1 parent 9ae066e commit 8aab977c14c9917ca38b4c4b60ebce241a12f2c6 @ctb ctb committed Oct 24, 2012
Showing with 78 additions and 241 deletions.
  1. +0 −139 recent-version/artifacts-paper2.bbl
  2. +78 −102 recent-version/artifacts-paper2.tex
@@ -1,139 +0,0 @@
-\begin{thebibliography}{10}
-\providecommand{\url}[1]{\texttt{#1}}
-\providecommand{\urlprefix}{URL }
-\expandafter\ifx\csname urlstyle\endcsname\relax
- \providecommand{\doi}[1]{doi:\discretionary{}{}{}#1}\else
- \providecommand{\doi}{doi:\discretionary{}{}{}\begingroup
- \urlstyle{rm}\Url}\fi
-\providecommand{\bibAnnoteFile}[1]{%
- \IfFileExists{#1}{\begin{quotation}\noindent\textsc{Key:} #1\\
- \textsc{Annotation:}\ \input{#1}\end{quotation}}{}}
-\providecommand{\bibAnnote}[2]{%
- \begin{quotation}\noindent\textsc{Key:} #1\\
- \textsc{Annotation:}\ #2\end{quotation}}
-\providecommand{\eprint}[2][]{\url{#2}}
-
-\bibitem{Hess:2011p686}
-Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, et~al. (2011) Metagenomic
- discovery of biomass-degrading genes and genomes from cow rumen.
-\newblock Science 331: 463--7.
-\bibAnnoteFile{Hess:2011p686}
-
-\bibitem{Qin:2010p189}
-Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et~al. (2010) A human gut
- microbial gene catalogue established by metagenomic sequencing.
-\newblock Nature 464: 59--65.
-\bibAnnoteFile{Qin:2010p189}
-
-\bibitem{Iverson:2012p1281}
-Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, et~al. (2012)
- Untangling genomes from metagenomes: revealing an uncultured class of marine
- euryarchaeota.
-\newblock Science 335: 587--90.
-\bibAnnoteFile{Iverson:2012p1281}
-
-\bibitem{Mackelprang:2011p1087}
-Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, et~al. (2011)
- Metagenomic analysis of a permafrost microbial community reveals a rapid
- response to thaw.
-\newblock Nature 480: 368--71.
-\bibAnnoteFile{Mackelprang:2011p1087}
-
-\bibitem{Miller:2010p226}
-Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation
- sequencing data.
-\newblock Genomics 95: 315--27.
-\bibAnnoteFile{Miller:2010p226}
-
-\bibitem{Pop:2009p798}
-Pop M (2009) Genome assembly reborn: recent computational challenges.
-\newblock Briefings in bioinformatics 10: 354--66.
-\bibAnnoteFile{Pop:2009p798}
-
-\bibitem{Mende:2012p1262}
-Mende DR, Waller AS, Sunagawa S, J{\"a}rvelin AI, Chan MM, et~al. (2012)
- Assessment of metagenomic assembly using simulated next generation sequencing
- data.
-\newblock PLoS ONE 7: e31386.
-\bibAnnoteFile{Mende:2012p1262}
-
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-Pignatelli M, Moya A (2011) Evaluating the fidelity of de novo short read
- metagenomic assembly using simulated data.
-\newblock PLoS ONE 6: e19984.
-\bibAnnoteFile{Pignatelli:2011p742}
-
-\bibitem{Peng:2011p898}
-Peng Y, Leung HCM, Yiu SM, Chin FYL (2011) Meta-idba: a de novo assembler for
- metagenomic data.
-\newblock Bioinformatics 27: i94--101.
-\bibAnnoteFile{Peng:2011p898}
-
-\bibitem{Mavromatis:2006p894}
-Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, et~al. (2006) Use of
- simulated data sets to evaluate the fidelity of metagenomic processing
- methods.
-\newblock Nature Methods 4: 495--500.
-\bibAnnoteFile{Mavromatis:2006p894}
-
-\bibitem{Morgan:2010p740}
-Morgan J, Darling A, Eisen J (2010) Metagenomic sequencing of an in
- vitro-simulated microbial community.
-\newblock PLoS ONE 5: e10209.
-\bibAnnoteFile{Morgan:2010p740}
-
-\bibitem{GomezAlvarez:2009p1334}
-Gomez-Alvarez V, Teal TK, Schmidt TM (2009) Systematic artifacts in metagenomes
- from complex microbial communities.
-\newblock The ISME Journal 3: 1314--7.
-\bibAnnoteFile{GomezAlvarez:2009p1334}
-
-\bibitem{Keegan:2012p1336}
-Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, et~al. (2012) A
- platform-independent method for detecting errors in metagenomic sequencing
- data: Drisee.
-\newblock PLoS Comput Biol 8: e1002541.
-\bibAnnoteFile{Keegan:2012p1336}
-
-\bibitem{Niu:2010p1333}
-Niu B, Fu L, Sun S, Li W (2010) Artificial and natural duplicates in
- pyrosequencing reads of metagenomic data.
-\newblock BMC Bioinformatics 11: 187.
-\bibAnnoteFile{Niu:2010p1333}
-
-\bibitem{Simpson:2009p233}
-Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, et~al. (2009) Abyss: a
- parallel assembler for short read sequence data.
-\newblock Genome Res 19: 1117--23.
-\bibAnnoteFile{Simpson:2009p233}
-
-\bibitem{Zerbino:2008p665}
-Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
- using de bruijn graphs.
-\newblock Genome Res 18: 821--9.
-\bibAnnoteFile{Zerbino:2008p665}
-
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-Barab{\'a}si A, Albert R (1999) Emergence of scaling in random networks.
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-\bibAnnoteFile{Barabasi:1999p1083}
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-Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment
- search tool.
-\newblock J Mol Biol 215: 403--10.
-\bibAnnoteFile{Altschul:1990p1335}
-
-\bibitem{Li:2001p1337}
-Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences
- to reduce the size of large protein databases.
-\newblock Bioinformatics 17: 282--3.
-\bibAnnoteFile{Li:2001p1337}
-
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-Sommer DD, Delcher AL, Salzberg SL, Pop M (2007) Minimus: a fast, lightweight
- genome assembler.
-\newblock Bmc Bioinformatics 8: 64.
-\bibAnnoteFile{Sommer:2007p1253}
-
-\end{thebibliography}
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