literatura.bib

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@inproceedings{cr_index,
  title={Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly},
  author={Bo{\v{z}}a, Vladim{\'\i}r and Jursa, Jakub and Brejov{\'a}, Bro{\v{n}}a and Vina{\v{r}}, Tom{\'a}{\v{s}}},
  booktitle={String Processing and Information Retrieval},
  pages={188--198},
  year={2015},
  organization={Springer}
}

@article{de_bruijn,
  title={A combinatorial problem},
  author={de Bruijn, NG},
  journal={Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen. Series A},
  volume={49},
  number={7},
  pages={758},
  year={1946}
}

@article{rural_postman_connected,
  title={Arc routing problems, part II: The rural postman problem},
  author={Eiselt, Horst A and Gendreau, Michel and Laporte, Gilbert},
  journal={Operations research},
  volume={43},
  number={3},
  pages={399--414},
  year={1995},
  publisher={INFORMS}
}

@article{superstring,
  title={On finding minimal length superstrings},
  author={Gallant, John and Maier, David and Astorer, James},
  journal={Journal of Computer and System Sciences},
  volume={20},
  number={1},
  pages={50--58},
  year={1980},
  publisher={Elsevier}
}

@article{gaml,
  title={{GAML}: genome assembly by maximum likelihood},
  author={Bo{\v{z}}a, Vladim{\'\i}r and Brejov{\'a}, Bro{\v{n}}a and Vina{\v{r}}, Tom{\'a}{\v{s}}},
  journal={Algorithms for Molecular Biology},
  volume={10},
  number={1},
  pages={1--10},
  year={2015},
  publisher={Springer}
}

@article{gk_arrays,
  title={Querying large read collections in main memory: a versatile data structure},
  author={Philippe, Nicolas and Salson, Mikael and Lecroq, Thierry and Leonard, Martine and Commes, Therese and Rivals, Eric},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={1},
  year={2011},
  publisher={BioMed Central}
}

@incollection{comp_gk_arrays,
  title={Scalable and versatile k-mer indexing for high-throughput sequencing data},
  author={V{\"a}lim{\"a}ki, Niko and Rivals, Eric},
  booktitle={Bioinformatics Research and Applications},
  pages={237--248},
  year={2013},
  publisher={Springer}
}

@article{ruralpostman,
  title={On general routing problems},
  author={Lenstra, Jan Karel and Kan, AHG},
  journal={Networks},
  volume={6},
  number={3},
  pages={273--280},
  year={1976},
  publisher={Wiley Online Library}
}

@article{chinesepostman,
  title={Matching, Euler tours and the Chinese postman},
  author={Edmonds, Jack and Johnson, Ellis L},
  journal={Mathematical programming},
  volume={5},
  number={1},
  pages={88--124},
  year={1973},
  publisher={Springer}
}

@article{mincost_maxflow,
  title={Theoretical improvements in algorithmic efficiency for network flow problems},
  author={Edmonds, Jack and Karp, Richard M},
  journal={Journal of the ACM (JACM)},
  volume={19},
  number={2},
  pages={248--264},
  year={1972},
  publisher={ACM}
}

@inproceedings{rrr_vector,
  title={Succinct indexable dictionaries with applications to encoding k-ary trees and multisets},
  author={Raman, Rajeev and Raman, Venkatesh and Rao, S Srinivasa},
  booktitle={Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms},
  pages={233--242},
  year={2002},
  organization={Society for Industrial and Applied Mathematics}
}

@article{integer_coding,
  title={Universal codeword sets and representations of the integers},
  author={Elias, Peter},
  journal={Information Theory, IEEE Transactions on},
  volume={21},
  number={2},
  pages={194--203},
  year={1975},
  publisher={IEEE}
}

@inproceedings{sdarray,
  title={Practical entropy-compressed rank/select dictionary},
  author={Okanohara, Daisuke and Sadakane, Kunihiko},
  booktitle={Proceedings of the Meeting on Algorithm Engineering \& Expermiments},
  pages={60--70},
  year={2007},
  organization={Society for Industrial and Applied Mathematics}
}

@inproceedings{fm_index,
  title={Opportunistic data structures with applications},
  author={Ferragina, Paolo and Manzini, Giovanni},
  booktitle={Foundations of Computer Science, 2000. Proceedings. 41st Annual Symposium on},
  pages={390--398},
  year={2000},
  organization={IEEE}
}

@inproceedings{sdsl,
  title     = {From Theory to Practice: Plug and Play with Succinct Data Structures},
  author    = {Gog, Simon and Beller, Timo and Moffat, Alistair and Petri, Matthias},
  booktitle = {13th International Symposium on Experimental Algorithms, (SEA 2014)},
  year      = {2014},
  pages     = {326-337},
  ee        = {http://dx.doi.org/10.1007/978-3-319-07959-2_28}
}

@article{gage,
  title={{GAGE}: A critical evaluation of genome assemblies and assembly algorithms},
  author={Salzberg, Steven L and Phillippy, Adam M and Zimin, Aleksey and Puiu, Daniela and Magoc, Tanja and Koren, Sergey and Treangen, Todd J and Schatz, Michael C and Delcher, Arthur L and Roberts, Michael and others},
  journal={Genome research},
  volume={22},
  number={3},
  pages={557--567},
  year={2012},
  publisher={Cold Spring Harbor Lab}
}