@MISC{Caporaso-Bolyen-2024,
  title        = "Developing with {QIIME} 2",
  author       = "{Caporaso, J Gregory and Bolyen, Evan}",
  year         =  2024,
  howpublished = "https://develop.qiime2.org"
}

@article{kang2019,
  title = {{{MetaBAT}} 2: {{An}} Adaptive Binning Algorithm for Robust and Efficient Genome Reconstruction from Metagenome Assemblies},
  author = {Kang, Dongwan D. and Li, Feng and Kirton, Edward and Thomas, Ashleigh and Egan, Rob and An, Hong and Wang, Zhong},
  year = {2019},
  journal = {PeerJ},
  volume = {2019},
  number = {7},
  publisher = {{PeerJ Inc.}},
  issn = {21678359},
  doi = {10.7717/peerj.7359},
  keywords = {Clustering,Metagenome binning,Metagenomics}
}

@article{manni_busco_2021,
	title = {{BUSCO} {Update}: {Novel} and {Streamlined} {Workflows} along with {Broader} and {Deeper} {Phylogenetic} {Coverage} for {Scoring} of {Eukaryotic}, {Prokaryotic}, and {Viral} {Genomes}},
	volume = {38},
	issn = {1537-1719},
	shorttitle = {{BUSCO} {Update}},
	url = {https://academic.oup.com/mbe/article/38/10/4647/6329644},
	doi = {10.1093/molbev/msab199},
	language = {en},
	number = {10},
	urldate = {2023-08-09},
	journal = {Molecular Biology and Evolution},
	author = {Manni, Mosè and Berkeley, Matthew R and Seppey, Mathieu and Simão, Felipe A and Zdobnov, Evgeny M},
	editor = {Kelley, Joanna},
	month = sep,
	year = {2021},
	pages = {4647--4654},
}

@article{heng2009samtools,
    author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup},
    title = {The Sequence Alignment/Map format and SAMtools},
    journal = {Bioinformatics},
    volume = {25},
    number = {16},
    pages = {2078-2079},
    year = {2009},
    month = {06},
    issn = {1367-4803},
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}

@misc{scikit_bio_release,
    title = {biocore/scikit-bio: scikit-bio 0.5.9: Maintenance release},
    year = {2023},
    publisher = {Zenodo},
    version = {0.5.9},
    doi = {10.5281/zenodo.8209901},
    url = {https://doi.org/10.5281/zenodo.8209901}
}

@article{pan_deep_2022,
	title = {A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments},
	volume = {13},
	rights = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-29843-y},
	doi = {10.1038/s41467-022-29843-y},
	pages = {2326},
	number = {1},
	journaltitle = {Nature Communications},
	shortjournal = {Nat Commun},
	publisher = {Nature Publishing Group},
	author = {Pan, Shaojun and Zhu, Chengkai and Zhao, Xing-Ming and Coelho, Luis Pedro},
	urldate = {2026-02-18},
	date = {2022-04-28},
	langid = {english},
	keywords = {Machine learning, Metagenomics},
}

@article{pan_semibin2_2023,
	title = {{SemiBin}2: self-supervised contrastive learning leads to better {MAGs} for short- and long-read sequencing},
	volume = {39},
	issn = {1367-4811},
	url = {https://doi.org/10.1093/bioinformatics/btad209},
	doi = {10.1093/bioinformatics/btad209},
	shorttitle = {{SemiBin}2},
	pages = {i21--i29},
	issue = {Supplement\_1},
	journaltitle = {Bioinformatics},
	shortjournal = {Bioinformatics},
	author = {Pan, Shaojun and Zhao, Xing-Ming and Coelho, Luis Pedro},
	urldate = {2026-02-18},
	date = {2023-06-01},
}
