Bibliography.bib

@article{garg_graph,
  title={A graph-based approach to diploid genome assembly.},
  author={Garg, S and Rautiainen, M and Novak, AM and Garrison, E and Durbin, R and Marschall, T},
  journal={Bioinformatics (Oxford, England)},
  volume={34},
  number={13},
  pages={i105--i114},
  year={2018},
  publisher={Oxford University Press}
}

@inproceedings{klau2017guided,
  title={A guided tour to computational haplotyping},
  author={Klau, Gunnar W and Marschall, Tobias},
  booktitle={Conference on Computability in Europe},
  pages={50--63},
  year={2017},
  organization={Springer}
}

@inproceedings{medvedev2007computability,
  title={Computability of models for sequence assembly},
  author={Medvedev, Paul and Georgiou, Konstantinos and Myers, Gene and Brudno, Michael},
  booktitle={International Workshop on Algorithms in Bioinformatics},
  pages={289--301},
  year={2007},
  organization={Springer}
}

@article{cilibrasi2007complexity,
  title={The complexity of the single individual SNP haplotyping problem},
  author={Cilibrasi, Rudi and Van Iersel, Leo and Kelk, Steven and Tromp, John},
  journal={Algorithmica},
  volume={49},
  number={1},
  pages={13--36},
  year={2007},
  publisher={Springer}
}

@article{crawford2005definition,
  title={Definition and clinical importance of haplotypes},
  author={Crawford, Dana C and Nickerson, Deborah A},
  journal={Annu. Rev. Med.},
  volume={56},
  pages={303--320},
  year={2005},
  publisher={Annual Reviews}
}

@article{browning2011haplotype,
  title={Haplotype phasing: existing methods and new developments},
  author={Browning, Sharon R and Browning, Brian L},
  journal={Nature Reviews Genetics},
  volume={12},
  number={10},
  pages={703},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{rhee2016survey,
  title={Survey of computational haplotype determination methods for single individual},
  author={Rhee, Je-Keun and Li, Honglan and Joung, Je-Gun and Hwang, Kyu-Baek and Zhang, Byoung-Tak and Shin, Soo-Yong},
  journal={Genes \& Genomics},
  volume={38},
  number={1},
  pages={1--12},
  year={2016},
  publisher={Springer}
}

@article{manolio2010genomewide,
  title={Genomewide association studies and assessment of the risk of disease},
  author={Manolio, Teri A},
  journal={New England journal of medicine},
  volume={363},
  number={2},
  pages={166--176},
  year={2010},
  publisher={Mass Medical Soc}
}

@inproceedings{lancia2001snps,
  title={SNPs problems, complexity, and algorithms},
  author={Lancia, Giuseppe and Bafna, Vineet and Istrail, Sorin and Lippert, Ross and Schwartz, Russell},
  booktitle={European symposium on algorithms},
  pages={182--193},
  year={2001},
  organization={Springer}
}

@article{bonizzoni2016minimum,
  title={On the minimum error correction problem for haplotype assembly in diploid and polyploid genomes},
  author={Bonizzoni, Paola and Dondi, Riccardo and Klau, Gunnar W and Pirola, Yuri and Pisanti, Nadia and Zaccaria, Simone},
  journal={Journal of Computational Biology},
  volume={23},
  number={9},
  pages={718--736},
  year={2016},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{sohn2016present,
    title = "{The present and future of de novo whole-genome assembly}",
    author = {Sohn, Jang-il and Nam, Jin-Wu},
    journal = {Briefings in Bioinformatics},
    volume = {19},
    number = {1},
    pages = {23-40},
    year = {2016},
    month = {10},
    doi = {10.1093/bib/bbw096},
    publisher={Briefings in Bioinformatics}
}

@article{miller2010assembly,
  title={Assembly algorithms for next-generation sequencing data},
  author={Miller, Jason R and Koren, Sergey and Sutton, Granger},
  journal={Genomics},
  volume={95},
  number={6},
  pages={315--327},
  year={2010},
  publisher={Elsevier}
}

@article{schlebusch2012next,
  title={Next generation shotgun sequencing and the challenges of de novo genome assembly},
  author={Schlebusch, Stephen and Illing, Nicola},
  journal={South African Journal of Science},
  volume={108},
  number={11-12},
  pages={62--70},
  year={2012},
  publisher={Academy of Science of South Africa}
}
%bcalm paper
@article{chikhi2016compacting,
  title={Compacting de Bruijn graphs from sequencing data quickly and in low memory},
  author={Chikhi, Rayan and Limasset, Antoine and Medvedev, Paul},
  journal={Bioinformatics},
  volume={32},
  number={12},
  pages={i201--i208},
  year={2016},
  publisher={Oxford University Press}
}

@article{compeau2011bruijn,
  title={Why are de Bruijn graphs useful for genome assembly?},
  author={Compeau, Phillip EC and Pevzner, Pavel A and Tesler, Glenn},
  journal={Nature biotechnology},
  volume={29},
  number={11},
  pages={987},
  year={2011},
  publisher={NIH Public Access}
}

@inproceedings{iliopoulos2016popping,
  title={Popping superbubbles and discovering clumps: recent developments in biological sequence analysis},
  author={Iliopoulos, Costas S and Kundu, Ritu and Mohamed, Manal and Vayani, Fatima},
  booktitle={International Workshop on Algorithms and Computation},
  pages={3--14},
  year={2016},
  organization={Springer}
}

@article{paten2018superbubbles,
  title={Superbubbles, ultrabubbles, and cacti},
  author={Paten, Benedict and Eizenga, Jordan M and Rosen, Yohei M and Novak, Adam M and Garrison, Erik and Hickey, Glenn},
  journal={Journal of Computational Biology},
  volume={25},
  number={7},
  pages={649--663},
  year={2018},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{heather2016sequence,
  title={The sequence of sequencers: The history of sequencing DNA},
  author={Heather, James M and Chain, Benjamin},
  journal={Genomics},
  volume={107},
  number={1},
  pages={1--8},
  year={2016},
  publisher={Elsevier}
}

@article{kececioglu1995combinatorial,
  title={Combinatorial algorithms for DNA sequence assembly},
  author={Kececioglu, John D and Myers, Eugene W},
  journal={Algorithmica},
  volume={13},
  number={1-2},
  pages={7},
  year={1995},
  publisher={Springer}
}

@article{pevzner2001eulerian,
  title={An Eulerian path approach to DNA fragment assembly},
  author={Pevzner, Pavel A and Tang, Haixu and Waterman, Michael S},
  journal={Proceedings of the national academy of sciences},
  volume={98},
  number={17},
  pages={9748--9753},
  year={2001},
  publisher={National Acad Sciences}
}

@inproceedings{onodera2013detecting,
  title={Detecting superbubbles in assembly graphs},
  author={Onodera, Taku and Sadakane, Kunihiko and Shibuya, Tetsuo},
  booktitle={International Workshop on Algorithms in Bioinformatics},
  pages={338--348},
  year={2013},
  organization={Springer}
}

@article{song2014lighter,
  title={Lighter: fast and memory-efficient sequencing error correction without counting},
  author={Song, Li and Florea, Liliana and Langmead, Ben},
  journal={Genome biology},
  volume={15},
  number={11},
  pages={509},
  year={2014},
  publisher={BioMed Central}
}

@article{koboldt2006distribution,
  title={Distribution of human SNPs and its effect on high-throughput genotyping},
  author={Koboldt, Daniel C and Miller, Raymond D and Kwok, Pui-Yan},
  journal={Human mutation},
  volume={27},
  number={3},
  pages={249--254},
  year={2006},
  publisher={Wiley Online Library}
}

@article{guo2005distribution,
  title={The distribution of SNPs in human gene regulatory regions},
  author={Guo, Yongjian and Jamison, D Curtis},
  journal={Bmc Genomics},
  volume={6},
  number={1},
  pages={140},
  year={2005},
  publisher={BioMed Central}
}

@article{melsted2014kmerstream,
	title={KmerStream: streaming algorithms for k-mer abundance estimation},
	author={Melsted, P{\'a}ll and Halld{\'o}rsson, Bjarni V},
	journal={Bioinformatics},
	volume={30},
	number={24},
	pages={3541--3547},
	year={2014},
	publisher={Oxford University Press}
}

@article{zerbino2008velvet,
	title={Velvet: algorithms for de novo short read assembly using de Bruijn graphs},
	author={Zerbino, Daniel R and Birney, Ewan},
	journal={Genome research},
	volume={18},
	number={5},
	pages={821--829},
	year={2008},
	publisher={Cold Spring Harbor Lab}
}

@article{rautiainen2018bit,
  title={Bit-parallel sequence-to-graph alignment},
  author={Rautiainen, Mikko and M{\"a}kinen, Veli and Marschall, Tobias},
  journal={bioRxiv},
  pages={323063},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}

@article{wick2015bandage,
  title={Bandage: interactive visualization of de novo genome assemblies},
  author={Wick, Ryan R and Schultz, Mark B and Zobel, Justin and Holt, Kathryn E},
  journal={Bioinformatics},
  volume={31},
  number={20},
  pages={3350--3352},
  year={2015},
  publisher={Oxford University Press}
}

@article{chikhi2013informed,
  title={Informed and automated k-mer size selection for genome assembly},
  author={Chikhi, Rayan and Medvedev, Paul},
  journal={Bioinformatics},
  volume={30},
  number={1},
  pages={31--37},
  year={2013},
  publisher={Oxford University Press}
}

@article{martin2016whatshap,
  title={WhatsHap: fast and accurate read-based phasing},
  author={Martin, Marcel and Patterson, Murray and Garg, Shilpa and Fischer, Sarah O and Pisanti, Nadia and Klau, Gunnar W and Schoenhuth, Alexander and Marschall, Tobias},
  journal={BioRxiv},
  pages={085050},
  year={2016},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{patterson2014whatshap,
  title={Whatshap: Haplotype assembly for future-generation sequencing reads},
  author={Patterson, Murray and Marschall, Tobias and Pisanti, Nadia and van Iersel, Leo and Stougie, Leen and Klau, Gunnar W and Sch{\"o}nhuth, Alexander},
  booktitle={International Conference on Research in Computational Molecular Biology},
  pages={237--249},
  year={2014},
  organization={Springer}
}

@article{lee2016third,
  title={Third-generation sequencing and the future of genomics},
  author={Lee, Hayan and Gurtowski, James and Yoo, Shinjae and Nattestad, Maria and Marcus, Shoshana and Goodwin, Sara and McCombie, W Richard and Schatz, Michael},
  journal={BioRxiv},
  pages={048603},
  year={2016},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{jain2019complexity,
  title={On the complexity of sequence to graph alignment},
  author={Jain, Chirag and Zhang, Haowen and Gao, Yu and Aluru, Srinivas},
  booktitle={International Conference on Research in Computational Molecular Biology},
  pages={85--100},
  year={2019},
  organization={Springer}
}

@article{bloom1970space,
  title={Space/time trade-offs in hash coding with allowable errors},
  author={Bloom, Burton H},
  journal={Communications of the ACM},
  volume={13},
  number={7},
  pages={422--426},
  year={1970},
  publisher={ACM}
}