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Chapter2.bib
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title={Reducing assembly complexity of microbial genomes with single-molecule sequencing},
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year={2013}
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title={Genome assembly forensics: finding the elusive mis-assembly},
author={Phillippy, A.M. and Schatz, M.C. and Pop, M.},
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number={3},
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@article{ABySS,
author={Simpson, J.T. and Wong, K. and Jackman, S. D. and Schein, J. E. and Jones, S. J. M. and Birol, .I},
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@article{Allpaths-LG,
author={Gnerre, S and Maccallum, I and Przybylski, D and Ribeiro, FJ and Burton, JN and Walker, BJ and Sharpe, T and Hall, G and Shea, TP and Sykes, S, et al.},
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author={Koren, S. and Treangen, T.J. and Pop, M.},
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pages={2964--2971},
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@article{CABOG,
author={Miller, J.R. and Delcher, A.L. and Koren, S. and Venter, E. and Walenz, B.P. and Brownley, A. and Johnson, J. and Li, K. and Mobarry, C. and Sutton, G.},
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@article{Lin2011simulatedData,
title={Comparative studies of de novo assembly tools for next-generation sequencing technologies},
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title={Comparing \emph{de novo} genome assembly: the long and short of it},
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title={A whole-genome assembly of Drosophila},
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year={2010}
}
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title={Genovo: \emph{de novo} assembly for metagenomes},
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year={2011}
}
@article{DNPTrapper,
title={DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions},
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}
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title={A probabilistic approach to sequence assembly validation},
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year={2001}
}
@article{MauveMetrics,
title={Mauve Assembly Metrics},
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pages={2756--2757},
year={2011}
}
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title={Assembly reconciliation},
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journal={Bioinformatics},
volume={24},
pages={42--45},
year={2008}
}
@article{Hawkeye,
title={Hawkeye: an interactive visual analytics tool for genome assemblies},
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journal={Genome Biol},
volume={8},
pages={R34},
year={2007}
}
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title={Assemblathon 1: A competitive assessment of de novo short read assembly methods},
author={Earl, D. and Bradnam, K. and John, J.S. and Darling, A. and Lin, D. and Fass, J. and Yu, H.O.K. and Buffalo, V. and Zerbino, D.R. and Diekhans, M. and others},
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volume={21},
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pages={2224--2241},
year={2011},
publisher={Cold Spring Harbor Lab}
}
@misc{SGA,
Author={SGA},
Howpublished={\url{https://github.com/jts/sga}},
}
@misc{Celera,
Author={The Celera Assembler webpage},
Howpublished={\url{http://wgs-assembler.sourceforge.net}},
}
@misc{MSR-CA,
Author={MSR--CA},
Howpublished={\url{http://www.genome.umd.edu/SR_CA_MANUAL.htm}},
}
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title={Maximum likelihood genome assembly},
author={Medvedev, P. and Brudno, M.},
journal={Journal of computational Biology},
volume={16},
number={8},
pages={1101--1116},
year={2009},
publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@article{bradnam2013assemblathon,
title={Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species},
author={Bradnam, Keith R and Fass, Joseph N and Alexandrov, Anton and Baranay, Paul and Bechner, Michael and Birol, {\.I}nan{\c{c}} and Boisvert10, S{\'e}bastien and Chapman, Jarrod A and Chapuis, Guillaume and Chikhi, Rayan and others},
journal={arXiv preprint arXiv:1301.5406},
year={2013}
}
@article{vezzi2012feature,
title={Feature-by-feature--evaluating de novo sequence assembly},
author={Vezzi, F. and Narzisi, G. and Mishra, B.},
journal={PloS one},
volume={7},
number={2},
pages={e31002},
year={2012},
publisher={Public Library of Science}
}
@article{kingsford2010assembly,
title={Assembly complexity of prokaryotic genomes using short reads},
author={Kingsford, C. and Schatz, M. and Pop, M.},
journal={BMC bioinformatics},
volume={11},
number={1},
pages={21},
year={2010},
publisher={BioMed Central Ltd}
}
@article{nagarajan2010finishing,
title={Finishing genomes with limited resources: lessons from an ensemble of microbial genomes},
author={Nagarajan, N. and Cook, C. and Di Bonaventura, M.P. and Ge, H. and Richards, A. and Bishop-Lilly, K. and DeSalle, R. and Read, T. and Pop, M.},
journal={BMC genomics},
volume={11},
number={1},
pages={242},
year={2010},
publisher={BioMed Central Ltd}
}
@article{fraser2002value,
title={The value of complete microbial genome sequencing (you get what you pay for)},
author={Fraser, C.M. and Eisen, J.A. and Nelson, K.E. and Paulsen, I.T. and Salzberg, S.L.},
journal={Journal of bacteriology},
volume={184},
number={23},
pages={6403--6405},
year={2002},
publisher={Am Soc Microbiol}
}
@article{branscomb2002high,
title={On the high value of low standards},
author={Branscomb, E. and Predki, P.},
journal={Journal of bacteriology},
volume={184},
number={23},
pages={6406--6409},
year={2002},
publisher={Am Soc Microbiol}
}
@article{chain2009genome,
title={Genome project standards in a new era of sequencing},
author={Chain, PSG and Grafham, DV and Fulton, RS and Fitzgerald, MG and Hostetler, J. and Muzny, D. and Ali, J. and Birren, B. and Bruce, DC and Buhay, C. and others},
journal={Science},
volume={326},
number={5950},
pages={236--237},
year={2009},
publisher={American Association for the Advancement of Science}
}
@article{zhou2007validation,
title={Validation of rice genome sequence by optical mapping},
author={Zhou, S. and Bechner, M.C. and Place, M. and Churas, C.P. and Pape, L. and Leong, S.A. and Runnheim, R. and Forrest, D.K. and Goldstein, S. and Livny, M. and others},
journal={BMC genomics},
volume={8},
number={1},
pages={278},
year={2007},
publisher={BioMed Central Ltd}
}
@article{adamidi2011novo,
title={De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics},
author={Adamidi, C. and Wang, Y. and Gruen, D. and Mastrobuoni, G. and You, X. and Tolle, D. and Dodt, M. and Mackowiak, S.D. and Gogol-Doering, A. and Oenal, P. and others},
journal={Genome research},
volume={21},
number={7},
pages={1193--1200},
year={2011},
publisher={Cold Spring Harbor Lab}
}
@article{clark2013ale,
title={ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies},
author={Clark, Scott and Egan, Rob and Frazier, Peter I and Wang, Zhong},
journal={Bioinformatics},
year={2013},
publisher={Oxford Univ Press}
}
@article{rahman2013cgal,
title={CGAL: computing genome assembly likelihoods},
author={Rahman, Atif and Pachter, Lior},
journal={Genome Biology},
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