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Chapter1.bib
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@article{FRC2011,
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year={2011},
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}
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title={Assembly reconciliation},
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year={2008},
publisher={Oxford Univ Press}
}
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title={Hawkeye: an interactive visual analytics tool for genome assemblies},
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volume={8},
number={3},
pages={R34},
year={2007},
publisher={BioMed Central Ltd}
}
@article{earl2011assemblathon,
title={Assemblathon 1: a competitive assessment of de novo short read assembly methods},
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number={12},
pages={2224--2241},
year={2011},
publisher={Cold Spring Harbor Lab}
}
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title={Efficient de novo assembly of large genomes using compressed data structures},
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journal={Genome research},
volume={22},
number={3},
pages={549--556},
year={2012},
publisher={Cold Spring Harbor Lab}
}
@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, Paul and Brudno, Michael},
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}
}
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title={Feature-by-feature--evaluating de novo sequence assembly},
author={Vezzi, Francesco and Narzisi, Giuseppe and Mishra, Bud},
journal={PloS one},
volume={7},
number={2},
pages={e31002},
year={2012},
publisher={Public Library of Science}
}
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title={Assembly complexity of prokaryotic genomes using short reads},
author={Kingsford, Carl and Schatz, Michael C and Pop, Mihai},
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, Niranjan and Cook, Christopher and Di Bonaventura, MariaPia and Ge, Hong and Richards, Allen and Bishop-Lilly, Kimberly A and DeSalle, Robert and Read, Timothy D and Pop, Mihai},
journal={BMC genomics},
volume={11},
number={1},
pages={242},
year={2010},
publisher={BioMed Central Ltd}
}
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title={The value of complete microbial genome sequencing (you get what you pay for)},
author={Fraser, Claire M and Eisen, Jonathan A and Nelson, Karen E and Paulsen, Ian T and Salzberg, Steven L},
journal={Journal of bacteriology},
volume={184},
number={23},
pages={6403--6405},
year={2002},
publisher={Am Soc Microbiol}
}
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title={On the high value of low standards},
author={Branscomb, Elbert and Predki, Paul},
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={Consortia, GSC and Consortia, HMP Jumpstart and Chain, PSG and Grafham, DV and Fulton, RS and FitzGerald, MG and Hostetler, J and Muzny, D and Detter, JC and Ali, J and others},
journal={Science (New York, NY)},
volume={326},
number={5950},
year={2009},
publisher={NIH Public Access}
}
@article{zhou2007validation,
title={Validation of rice genome sequence by optical mapping},
author={Zhou, Shiguo and Bechner, Michael C and Place, Michael and Churas, Chris P and Pape, Louise and Leong, Sally A and Runnheim, Rod and Forrest, Dan K and Goldstein, Steve and Livny, Miron and others},
journal={BMC genomics},
volume={8},
number={1},
pages={278},
year={2007},
publisher={BioMed Central Ltd}
}
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title={De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics},
author={Adamidi, Catherine and Wang, Yongbo and Gruen, Dominic and Mastrobuoni, Guido and You, Xintian and Tolle, Dominic and Dodt, Matthias and Mackowiak, Sebastian D and Gogol-Doering, Andreas and Oenal, Pinar 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},
pages={bts723},
year={2013},
publisher={Oxford Univ Press}
}
@article{rahman2013cgal,
title={{CGAL}: computing genome assembly likelihoods},
author={Rahman, Atif and Pachter, Lior},
journal={Genome Biology},
volume={14},
number={1},
pages={R8},
year={2013}
}
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title={Against a whole-genome shotgun},
author={Green, Philip},
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volume={7},
number={5},
pages={410--417},
year={1997},
publisher={Cold Spring Harbor Lab}
}
@article{weber1997human,
title={Human whole-genome shotgun sequencing},
author={Weber, James L and Myers, Eugene W},
journal={Genome Research},
volume={7},
number={5},
pages={401--409},
year={1997},
publisher={Cold Spring Harbor Lab}
}
@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}
}
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title={Basic local alignment search tool},
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journal={Journal of molecular biology},
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