@InProceedings{ mckinney-proc-scipy-2010,
  author    = { Wes McKinney },
  title     = { Data Structures for Statistical Computing in Python },
  booktitle = { Proceedings of the 9th Python in Science Conference },
  pages     = { 51 -- 56 },
  year      = { 2010 },
  editor    = { St{\'e}fan van der Walt and Jarrod Millman }
}

@article{wood2019,
	title = {Improved metagenomic analysis with {Kraken} 2},
	volume = {20},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-019-1891-0},
	doi = {10.1186/s13059-019-1891-0},
	number = {1},
	urldate = {2023-01-17},
	journal = {Genome Biology},
	author = {Wood, Derrick E. and Lu, Jennifer and Langmead, Ben},
	month = {nov},
	year = {2019},
	keywords = {Alignment-free methods, Metagenomics, Metagenomics classification, Microbiome, Minimizers, Probabilistic data structures},
	pages = {257},
}

@article{lu2017,
  title = {Bracken: Estimating Species Abundance in Metagenomics Data},
  shorttitle = {Bracken},
  author = {Lu, Jennifer and Breitwieser, Florian P. and Thielen, Peter and Salzberg, Steven L.},
  year = {2017},
  month = jan,
  journal = {PeerJ Computer Science},
  volume = {3},
  pages = {e104},
  publisher = {{PeerJ Inc.}},
  issn = {2376-5992},
  doi = {10.7717/peerj-cs.104},
}

@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{menzel2016,
  title = {Fast and Sensitive Taxonomic Classification for Metagenomics with {{Kaiju}}},
  author = {Menzel, Peter and Ng, Kim Lee and Krogh, Anders},
  year = {2016},
  month = apr,
  journal = {Nature Communications},
  volume = {7},
  number = {1},
  pages = {11257},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/ncomms11257},
  keywords = {Classification and taxonomy,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{hyatt_prodigal_2010,
	title = {Prodigal: prokaryotic gene recognition and translation initiation site identification},
	volume = {11},
	issn = {1471-2105},
	shorttitle = {Prodigal},
	url = {https://doi.org/10.1186/1471-2105-11-119},
	doi = {10.1186/1471-2105-11-119},
	number = {1},
	urldate = {2023-10-23},
	journal = {BMC Bioinformatics},
	author = {Hyatt, Doug and Chen, Gwo-Liang and LoCascio, Philip F. and Land, Miriam L. and Larimer, Frank W. and Hauser, Loren J.},
	month = mar,
	year = {2010},
	keywords = {Bias Score, Codon Position, Halobacterium Salinarum, Ribosomal Binding Site, Translation Initiation Site},
	pages = {119},
}

@article{buchfink_sensitive_2021,
	title = {Sensitive protein alignments at tree-of-life scale using {DIAMOND}},
	volume = {18},
	copyright = {2021 The Author(s)},
	issn = {1548-7105},
	url = {https://www.nature.com/articles/s41592-021-01101-x},
	doi = {10.1038/s41592-021-01101-x},
	language = {en},
	number = {4},
	urldate = {2023-12-01},
	journal = {Nature Methods},
	author = {Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg},
	month = apr,
	year = {2021},
	note = {Number: 4},
	publisher = {{Nature Publishing Group}},
	keywords = {Computational biology and bioinformatics, Genome informatics, Genomic analysis, Sequencing, Software},
	pages = {366--368},
}

@misc{NCBI,
  title = {National Center for Biotechnology Information (NCBI)},
  url = {https://www.ncbi.nlm.nih.gov/},
  note = {Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information;},
}

@article{huerta_cepas_eggnog_2019,
	title = {{eggNOG} 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},
	volume = {47},
	issn = {0305-1048},
	shorttitle = {{eggNOG} 5.0},
	url = {https://doi.org/10.1093/nar/gky1085},
	doi = {10.1093/nar/gky1085},
	number = {D1},
	urldate = {2024-01-18},
	journal = {Nucleic Acids Research},
	author = {Huerta-Cepas, Jaime and Szklarczyk, Damian and Heller, Davide and Hernández-Plaza, Ana and Forslund, Sofia K and Cook, Helen and Mende, Daniel R and Letunic, Ivica and Rattei, Thomas and Jensen, Lars J and von Mering, Christian and Bork, Peer},
	month = jan,
	year = {2019},
	pages = {D309--D314},
}

@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},
    doi = {10.1093/bioinformatics/btp352},
    url = {https://doi.org/10.1093/bioinformatics/btp352},
}

@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}
}
