paper.bib

@article{benson2012genbank,
  title={GenBank},
  author={Benson, Dennis A and Cavanaugh, Mark and Clark, Karen and Karsch-Mizrachi, Ilene and Lipman, David J and Ostell, James and Sayers, Eric W},
  journal={Nucleic acids research},
  volume={41},
  number={D1},
  pages={D36--D42},
  year={2012},
  doi={10.1093/nar/gks1195},
  publisher={Oxford University Press}
}

@article{roberts2004reducing,
  title={Reducing storage requirements for biological sequence comparison},
  author={Roberts, Michael and Hayes, Wayne and Hunt, Brian R and Mount, Stephen M and Yorke, James A},
  journal={Bioinformatics},
  volume={20},
  number={18},
  pages={3363--3369},
  year={2004},
  doi={10.1093/bioinformatics/bth408},
  publisher={Oxford University Press}
}

@article{wood2014kraken,
  title={Kraken: ultrafast metagenomic sequence classification using exact alignments},
  author={Wood, Derrick E. and Salzberg, Steven L.},
  journal={Genome Biology},
  volume={15},
  number={3},
  pages={1--12},
  year={2014},
  doi={10.1186/gb-2014-15-3-r46},
  publisher={BioMed Central}
}

@article{breitwieser2018krakenuniq,
  title={Kraken{U}niq: confident and fast metagenomics classification using unique k-mer counts},
  author={Breitwieser, F.P. and Baker, D.N. and Salzberg, S.L.},
  journal={Genome Biology},
  volume={19},
  number={1},
  pages={1--10},
  year={2018},
  doi={10.1186/s13059-018-1568-0},
  publisher={BioMed Central}
}

@article{wood2019improved,
  title={Improved metagenomic analysis with Kraken 2},
  author={Wood, Derrick E. and Lu, Jennifer and Langmead, Ben},
  journal={Genome Biology},
  volume={20},
  number={1},
  pages={1--13},
  year={2019},
  doi={10.1186/s13059-019-1891-0},
  publisher={Springer}
}

@article{lu2018removing,
  title={Removing contaminants from databases of draft genomes},
  author={Lu, Jennifer and Salzberg, Steven L.},
  journal={PLoS Computational Biology},
  volume={14},
  number={6},
  pages={e1006277},
  year={2018},
  doi={10.1371/journal.pcbi.1006277},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{salzberg-pardo2016,
title={Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system},
author={Salzberg, SL and Breitwieser, FP and Kumar, A and Hao, H and Burger, P and Rodriguez, FJ and Lim, M and Quiñones-Hinojosa, A and Gallia, GL and Tornheim, JA and Melia, MT and Sears, CL and Pardo, CA},
journal={Neurology: Neuroimmunology and Neuroinflammation},
volume={3},
number={4},
pages={e251},
year={2016},
PMID={27340685}
}