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paper.bib
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@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}
}