@article {Robeson2021rescript,
  author = {Robeson, Michael S and O{\textquoteright}Rourke, Devon R and Kaehler, Benjamin D and Ziemski, Michal and Dillon, Matthew R and Foster, Jeffrey T and Bokulich, Nicholas A},
  title = {RESCRIPt: Reproducible sequence taxonomy reference database management},
  journal = {PLoS Computational Biology},
  year = {2021},
  doi = {10.1371/journal.pcbi.1009581},
  publisher = {Public Library of Science},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1009581}
}

@article{rognes2016vsearch,
  title={VSEARCH: a versatile open source tool for metagenomics},
  author={Rognes, Torbj{\o}rn and Flouri, Tom{\'a}{\v{s}} and Nichols, Ben and Quince, Christopher and Mah{\'e}, Fr{\'e}d{\'e}ric},
  journal={PeerJ},
  volume={4},
  pages={e2584},
  year={2016},
  publisher={PeerJ Inc.},
  doi={10.7717/peerj.2584}
}

@article{bokulich2018optimizing,
  author={Bokulich, Nicholas A. and Kaehler, Benjamin D. and Rideout, Jai Ram and Dillon, Matthew and Bolyen, Evan and Knight, Rob and Huttley, Gavin A. and Caporaso, J. Gregory},
  title={Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin},
  journal={Microbiome},
  year={2018},
  volume={6},
  number={1},
  pages={90},
  doi={10.1186/s40168-018-0470-z},
  url={https://doi.org/10.1186/s40168-018-0470-z}
}

@article{bokulich2017q2,
  title={q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data},
  author={Bokulich, Nicholas A. and Dillon, Matthew R. and Zhang, Yilong and Rideout, Jai Ram and Bolyen, Evan and Li, Huilin and Albert, Paul S. and Caporaso, J. Gregory},
  journal={mSystems},
  volume={3},
  number={6},
  pages={e00219-18},
  year={2018},
  doi={10.1128/mSystems.00219-18}
}


@article{Pruesse2007,
  title={SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB},
  author={Pruesse, Elmar and Quast, Christian and Knittel, Katrin and Fuchs, Bernhard M and Ludwig, Wolfgang and Peplies, Jorg and Glockner, Frank Oliver},
  journal={Nucleic Acids Res},
  volume={35},
  number={21},
  pages={7188-7196},
  year={2007},
}


@article{Quast2013,
  title={The SILVA ribosomal RNA gene database project: improved data processing and web-based tools},
  author={Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken, Jan and Schweer, Timmy and Yarza, Pablo and Peplies, Jorg and Glockner, Frank Oliver},
  journal= {Nucleic Acids Res},
  publisher={Oxford University Press},
  volume={41},
  number={Database issue},
  pages={D590-6},
  year={2013},
}

@article{ncbi2018database,
  title={Database resources of the national center for biotechnology information},
  author={NCBI Resource Coordinators},
  journal={Nucleic acids research},
  volume={46},
  number={D1},
  pages={D8--D13},
  year={2018},
  publisher={Oxford University Press},
  doi = {10.1093/nar/gkx1095},
  url = {https://doi.org/10.1093/nar/gkx1095}
}

@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},
  publisher={Oxford University Press}
}

@article{Parks2020gtdb,
  title={A complete domain-to-species taxonomy for Bacteria and Archaea.},
  author={Parks, Donovan H. and Chuvochina, Maria and Chaumeil, Pierre-Alain and Rinke, Christian and Mussig, Aaron J. and Hugenholtz, Philip},
  journal={Nature Biotechnology},
  volume={38},
  pages={1079-1086},
  year={2020},
  doi={10.1038/s41587-020-0501-8},
  url={https://doi.org/10.1038/s41587-020-0501-8}
  }

@article{Parks2021gtdb,
    author = {Parks, Donovan H and Chuvochina, Maria and Rinke, Christian and Mussig, Aaron J and Chaumeil, Pierre-Alain and Hugenholtz, Philip},
    title = "{GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy}",
    journal = {Nucleic Acids Research},
    volume = {50},
    number = {D1},
    pages = {D785-D794},
    year = {2021},
    month = {09},
    issn = {0305-1048},
    doi = {10.1093/nar/gkab776},
    url = {https://doi.org/10.1093/nar/gkab776},
    eprint = {https://academic.oup.com/nar/article-pdf/50/D1/D785/42058271/gkab776\_supplemental\_file.pdf},
}

@article{clark2016,
  title = {GenBank},
  author = {Clark, Karen and {Karsch-Mizrachi}, Ilene and Lipman, David J. and Ostell, James and Sayers, Eric W.},
  year = {2016},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {44},
  number = {D1},
  pages = {D67-72},
  issn = {1362-4962},
  doi = {10.1093/nar/gkv1276},
  pmcid = {PMC4702903},
  pmid = {26590407},
}

@article{oleary2016,
  title = {Reference Sequence ({{RefSeq}}) Database at {{NCBI}}: Current Status, Taxonomic Expansion, and Functional Annotation},
  shorttitle = {Reference Sequence ({{RefSeq}}) Database at {{NCBI}}},
  author = {O'Leary, Nuala A. and Wright, Mathew W. and Brister, J. Rodney and Ciufo, Stacy and Haddad, Diana and McVeigh, Rich and Rajput, Bhanu and Robbertse, Barbara and {Smith-White}, Brian and {Ako-Adjei}, Danso and Astashyn, Alexander and Badretdin, Azat and Bao, Yiming and Blinkova, Olga and Brover, Vyacheslav and Chetvernin, Vyacheslav and Choi, Jinna and Cox, Eric and Ermolaeva, Olga and Farrell, Catherine M. and Goldfarb, Tamara and Gupta, Tripti and Haft, Daniel and Hatcher, Eneida and Hlavina, Wratko and Joardar, Vinita S. and Kodali, Vamsi K. and Li, Wenjun and Maglott, Donna and Masterson, Patrick and McGarvey, Kelly M. and Murphy, Michael R. and O'Neill, Kathleen and Pujar, Shashikant and Rangwala, Sanjida H. and Rausch, Daniel and Riddick, Lillian D. and Schoch, Conrad and Shkeda, Andrei and Storz, Susan S. and Sun, Hanzhen and {Thibaud-Nissen}, Francoise and Tolstoy, Igor and Tully, Raymond E. and Vatsan, Anjana R. and Wallin, Craig and Webb, David and Wu, Wendy and Landrum, Melissa J. and Kimchi, Avi and Tatusova, Tatiana and DiCuccio, Michael and Kitts, Paul and Murphy, Terence D. and Pruitt, Kim D.},
  year = {2016},
  month = jan,
  journal = {Nucleic Acids Research},
  volume = {44},
  number = {D1},
  pages = {D733-745},
  issn = {1362-4962},
  doi = {10.1093/nar/gkv1189},
  pmcid = {PMC4702849},
  pmid = {26553804},
}

@article{schoch2020,
  title = {{{NCBI Taxonomy}}: A Comprehensive Update on Curation, Resources and Tools},
  shorttitle = {{{NCBI Taxonomy}}},
  author = {Schoch, Conrad L and Ciufo, Stacy and Domrachev, Mikhail and Hotton, Carol L and Kannan, Sivakumar and Khovanskaya, Rogneda and Leipe, Detlef and Mcveigh, Richard and O'Neill, Kathleen and Robbertse, Barbara and Sharma, Shobha and Soussov, Vladimir and Sullivan, John P and Sun, Lu and Turner, Se{\'a}n and {Karsch-Mizrachi}, Ilene},
  year = {2020},
  month = aug,
  journal = {Database: The Journal of Biological Databases and Curation},
  volume = {2020},
  pages = {baaa062},
  issn = {1758-0463},
  doi = {10.1093/database/baaa062},
  urldate = {2023-04-18},
  pmcid = {PMC7408187},
  pmid = {32761142}
}

@article{nilsson2019unite,
  author = {Nilsson, Rolf Henrik and Larsson, Karl-Henrik and Taylor, Andy F S and Bengtsson-Palme, Johan and Jeppesen, Thomas S and Schigel, Dmitry and Kennedy, Peter and Picard, Kathryn and Glöckner, Frank Oliver and Tedersoo, Leho and Saar, Irja and Kõljalg, Urmas and Abarenkov, Kessy},
  title = "{The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications}",
  journal = {Nucleic Acids Research},
  volume = {47},
  number = {D1},
  pages = {D259-D264},
  year = {2018},
  month = {10},
  issn = {0305-1048},
  doi = {10.1093/nar/gky1022},
  url = {https://doi.org/10.1093/nar/gky1022},
  eprint = {https://academic.oup.com/nar/article-pdf/47/D1/D259/27436038/gky1022.pdf},
  pmcid = {PMC6324048},
  pmid = {30371820},
}
