@article{Ondov:2015,
  title={Fast genome and metagenome distance estimation using MinHash},
  author={Ondov, Brian D and Treangen, Todd J and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
  journal={bioRxiv},
  pages={029827},
  year={2015},
  publisher={Cold Spring Harbor Labs Journals},
  doi={10.1101/029827},
  url={https://doi.org/10.1101/029827}
}

@article{Brown:2016,
  doi = {10.21105/joss.00027},
  url = {https://doi.org/10.21105/joss.00027},
  year = {2016},
  publisher = {The Open Journal},
  volume = {1},
  number = {5},
  pages = {27},
  author = {C. Titus Brown and Luiz Irber},
  title = {sourmash: a library for MinHash sketching of DNA},
  journal = {Journal of Open Source Software}
}

@article{Pierce:2019,
  doi = {10.12688/f1000research.19675.1},
  url = {https://doi.org/10.12688/f1000research.19675.1},
  year = {2019},
  month = jul,
  publisher = {F1000 Research Ltd},
  volume = {8},
  pages = {1006},
  author = {N. Tessa Pierce and Luiz Irber and Taylor Reiter and Phillip Brooks and C. Titus Brown},
  title = {Large-scale sequence comparisons with sourmash},
  journal = {F1000Research}
}

@article{gather,
  doi = {10.1101/2022.01.11.475838},
  url = {https://doi.org/10.1101/2022.01.11.475838},
  title={Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers},
  author={Irber, Luiz Carlos and Brooks, Phillip T and Reiter, Taylor E and Pierce-Ward, N Tessa and Hera, Mahmudur Rahman and Koslicki, David and Brown, C Titus},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{branchwater,
  doi = {10.1101/2022.11.02.514947},
  url={https://doi.org/10.1101/2022.11.02.514947},
  title={Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search},
  author={Irber, Luiz Carlos and Pierce-Ward, N Tessa and Brown, C Titus},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{koslicki2019improving,
  doi={10.1016/j.amc.2019.02.018},
  url={https://doi.org/10.1016/j.amc.2019.02.018},
  title={Improving minhash via the containment index with applications to metagenomic analysis},
  author={Koslicki, David and Zabeti, Hooman},
  journal={Applied Mathematics and Computation},
  volume={354},
  pages={206--215},
  year={2019},
  publisher={Elsevier}
}

@article{hera2023deriving,
  doi={10.1101/gr.277651.123},
  url={https://doi.org/10.1101/gr.277651.123},
  title={Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash},
  author={Rahman Hera, Mahmudur and Pierce-Ward, N Tessa and Koslicki, David},
  journal={Genome Research},
  pages={gr--277651},
  year={2023},
  publisher={Cold Spring Harbor Lab}
}

@article{hera2023fast,
  doi = {10.1101/2023.11.06.565843},
  url = {https://doi.org/10.1101/2023.11.06.565843},
  title={Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches},
  author={Rahman Hera, Mahmudur and Liu, Shaopeng and Wei, Wei and Rodriguez, Judith S and Ma, Chunyu and Koslicki, David},
  journal={bioRxiv},
  pages={2023--11},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

@article{portik2022evaluation,
  doi={10.1186/s12859-022-05103-0},
  url={https://doi.org/10.1186/s12859-022-05103-0},
  title={Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets},
  author={Portik, Daniel M and Brown, C Titus and Pierce-Ward, N Tessa},
  journal={Bioinformatics},
  year={2022}
}
