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@article{computational2016computational,
title={Computational pan-genomics: status, promises and challenges},
author={{Computational pan-genomics consortium}},
journal={Briefings in Bioinformatics},
volume={19},
number={1},
pages={118--135},
year={2016},
publisher={Oxford University Press}
}
@article{Pevzner_2001,
title={An {E}ulerian path approach to {DNA} fragment assembly},
volume={98},
ISSN={1091-6490},
url={http://dx.doi.org/10.1073/pnas.171285098},
DOI={10.1073/pnas.171285098},
number={17},
journal={Proceedings of the National Academy of Sciences},
publisher={Proceedings of the National Academy of Sciences},
author={Pevzner, P. A. and Tang, H. and Waterman, M. S.},
year={2001},
month={Aug},
pages={9748–9753}
}
@article{Paten_2017,
title={Genome graphs and the evolution of genome inference},
volume={27},
ISSN={1549-5469},
url={http://dx.doi.org/10.1101/gr.214155.116},
DOI={10.1101/gr.214155.116},
number={5},
journal={Genome Research},
publisher={Cold Spring Harbor Laboratory},
author={Paten, Benedict and Novak, Adam M. and Eizenga, Jordan M. and Garrison, Erik},
year={2017},
month={Mar},
pages={665–676}
}
@article{kehr2014genome,
title={Genome alignment with graph data structures: a comparison},
author={Kehr, Birte and Trappe, Kathrin and Holtgrewe, Manuel and Reinert, Knut},
journal={BMC Bioinformatics},
volume={15},
number={1},
pages={99},
year={2014},
publisher={BioMed Central}
}
@article{Garrison_2018,
title={Variation graph toolkit improves read mapping by representing genetic variation in the reference},
volume={36},
ISSN={1546-1696},
url={http://dx.doi.org/10.1038/nbt.4227},
DOI={10.1038/nbt.4227},
number={9},
journal={Nature Biotechnology},
publisher={Springer Science and Business Media LLC},
author={Garrison, Erik and Sirén, Jouni and Novak, Adam M and Hickey, Glenn and Eizenga, Jordan M and Dawson, Eric T and Jones, William and Garg, Shilpa and Markello, Charles and Lin, Michael F and et al.},
year={2018},
month={Aug},
pages={875–879}
}
@phdthesis{Garrison_2019,
title={Graphical pangenomics},
author={Garrison, Erik},
year={2019},
school={University of Cambridge}
}
@inproceedings{gbmp2014sea,
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}
}
@inproceedings{prezza2017framework,
title={A Framework of Dynamic Data Structures for String Processing},
author={Prezza, Nicola.},
booktitle={International Symposium on Experimental Algorithms},
year={2017},
organization={Leibniz International Proceedings in Informatics (LIPIcs)}
}
@article{Siren_2019,
title={Haplotype-aware graph indexes},
author={Sir{\'e}n, Jouni and Garrison, Erik and Novak, Adam M and Paten, Benedict and Durbin, Richard},
journal={Bioinformatics},
volume={36},
number={2},
pages={400--407},
year={2020},
publisher={Oxford University Press}
}
@article{chaisson2019multi,
title={Multi-platform discovery of haplotype-resolved structural variation in human genomes},
author={Chaisson, Mark JP and Sanders, Ashley D and Zhao, Xuefang and Malhotra, Ankit and Porubsky, David and Rausch, Tobias and Gardner, Eugene J and Rodriguez, Oscar L and Guo, Li and Collins, Ryan L and others},
journal={{Nature Communications}},
volume={10},
number={1},
pages={1784},
year={2019},
publisher={Nature Publishing Group},
doi={10.1038/s41467-018-08148-z}
}
@article{hickey2020genotyping,
title={Genotyping structural variants in pangenome graphs using the vg toolkit},
author={Hickey, Glenn and Heller, David and Monlong, Jean and Sibbesen, Jonas A and Sir{\'e}n, Jouni and Eizenga, Jordan and Dawson, Eric T and Garrison, Erik and Novak, Adam M and Paten, Benedict},
journal={{Genome Biology}},
volume={21},
number={1},
pages={1--17},
year={2020},
publisher={BioMed Central}
}
@article{crysnanto2019sequence,
title={Sequence read mapping and variant discovery from bovine breed-specific augmented reference graphs},
author={Crysnanto, Danang and Pausch, Hubert},
journal={bioRxiv},
year={2019},
publisher={Cold Spring Harbor Laboratory}
}
@article{garg2018graph,
title={A graph-based approach to diploid genome assembly},
author={Garg, Shilpa and Rautiainen, Mikko and Novak, Adam M and Garrison, Erik and Durbin, Richard and Marschall, Tobias},
journal={Bioinformatics},
volume={34},
number={13},
pages={i105--i114},
year={2018},
publisher={Oxford University Press}
}
@misc{pybind11,
author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
year = {2017},
note = {https://github.com/pybind/pybind11},
title = {pybind11 -- Seamless operability between C++11 and Python}
}
@article{brehm2019hash,
title={Hash Tables with Pseudorandom Global Order},
author={Brehm, Wolfgang},
journal={INFOCOMP Journal of Computer Science},
volume={18},
number={1},
pages={20--25},
year={2019}
}