
@article{Pallen2010,
abstract = {High-throughput sequencing is sweeping through clinical microbiology, transforming our discipline in its wake. It is already providing an enhanced view of pathogen biology through rapid and inexpensive whole-genome sequencing and more sophisticated applications such as RNA-seq. It also promises to deliver high-resolution genomic epidemiology as the ultimate typing method for bacteria. However, the most revolutionary effect of this 'disruptive technology' is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming 'technological singularity' in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.},
author = {Pallen, Mark J and Loman, Nicholas J and Penn, Charles W},
doi = {10.1016/j.mib.2010.08.003},
issn = {1879-0364},
journal = {Current opinion in microbiology},
keywords = {Gene Expression Profiling,Genome, Bacterial,Genotype,High-Throughput Nucleotide Sequencing,Microbiological Techniques,Microbiological Techniques: methods,Phenotype,Sequence Analysis, DNA,Sequence Analysis, RNA},
month = {oct},
number = {5},
pages = {625--31},
pmid = {20843733},
publisher = {Elsevier Ltd},
title = {{High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20843733},
volume = {13},
year = {2010}
}

@article{uniprot2018uniprot,
  title={UniProt: the universal protein knowledgebase},
  author={UniProt Consortium and others},
  journal={Nucleic acids research},
  volume={46},
  number={5},
  pages={2699},
  year={2018},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pubmed/29425356}
}

@article{blanco2018blasterjs,
	title={BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results},
	author={Blanco-M{\'\i}guez, Aitor and Fdez-Riverola, Florentino and S{\'a}nchez, Borja and Louren{\c{c}}o, An{\'a}lia},
 	journal={PLoS One},
	volume={13},
	number={10},
	pages={e0205286},
	year={2018},
	publisher={Public Library of Science San Francisco, CA USA},
	url={https://pubmed.ncbi.nlm.nih.gov/30300406/}
}

@article{parks2015checkm,
	title={CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes},
	author={Parks, Donovan H and Imelfort, Michael and Skennerton, Connor T and Hugenholtz, Philip and Tyson, Gene W},
	journal={Genome research},
	volume={25},
	number={7},
	pages={1043--1055},
	year={2015},
	publisher={Cold Spring Harbor Lab},
	url={https://pubmed.ncbi.nlm.nih.gov/25977477/}
}

@article{altschul1990basic,
	title={Basic local alignment search tool},
	author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
	journal={Journal of molecular biology},
	volume={215},
	number={3},
	pages={403--410},
	year={1990},
	publisher={Elsevier},
	url={https://pubmed.ncbi.nlm.nih.gov/2231712/}
}

@article{lu2020cdd,
	title={CDD/SPARCLE: the conserved domain database in 2020},
	author={Lu, Shennan and Wang, Jiyao and Chitsaz, Farideh and Derbyshire, Myra K and Geer, Renata C and Gonzales, Noreen R and Gwadz, Marc and Hurwitz, David I and Marchler, Gabriele H and Song, James S and others},
	journal={Nucleic acids research},
	volume={48},
	number={D1},
	pages={D265--D268},
	year={2020},
	publisher={Oxford University Press},
	url={https://pubmed.ncbi.nlm.nih.gov/31777944/}
}

@article{aramaki2020kofamkoala,
	title={KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold},
	author={Aramaki, Takuya and Blanc-Mathieu, Romain and Endo, Hisashi and Ohkubo, Koichi and Kanehisa, Minoru and Goto, Susumu and Ogata, Hiroyuki},
	journal={Bioinformatics},
	volume={36},
	number={7},
	pages={2251--2252},
	year={2020},
	publisher={Oxford University Press},
	url={https://pubmed.ncbi.nlm.nih.gov/31742321/}
}

@article{buchfink2021sensitive,
	title={Sensitive protein alignments at tree-of-life scale using DIAMOND},
	author={Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg},
	journal={Nature methods},
	volume={18},
	number={4},
	pages={366--368},
	year={2021},
	publisher={Nature Publishing Group},
	url={https://pubmed.ncbi.nlm.nih.gov/33828273/}
}


@article{kanehisa2015kegg,
  title={KEGG as a reference resource for gene and protein annotation},
  author={Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D457--D462},
  year={2015},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pubmed/26476454}
}

@article{bardou2014jvenn,
  title={jvenn: an interactive Venn diagram viewer},
  author={Bardou, Philippe and Mariette, Jérôme and Escudié, Fédéric and Djemiel, Christophe and Klopp, Christophe},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={293},
  year={2014},
  publisher={BioMed Central},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261873/}
}

@article{huerta2016ete,
  title={ETE 3: reconstruction, analysis, and visualization of phylogenomic data},
  author={Huerta-Cepas, Jaime and Serra, François and Bork, Peer},
  journal={Molecular biology and evolution},
  volume={33},
  number={6},
  pages={1635--1638},
  year={2016},
  publisher={Society for Molecular Biology and Evolution},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116/}
}



@article{finn2015pfam,
  title={The Pfam protein families database: towards a more sustainable future},
  author={Finn, Robert D and Coggill, Penelope and Eberhardt, Ruth Y and Eddy, Sean R and Mistry, Jaina and Mitchell, Alex L and Potter, Simon C and Punta, Marco and Qureshi, Matloob and Sangrador-Vegas, Amaia and others},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D279--D285},
  year={2015},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702930/}
}

@article{galperin2014expanded,
  title={Expanded microbial genome coverage and improved protein family annotation in the COG database},
  author={Galperin, Michael Y and Makarova, Kira S and Wolf, Yuri I and Koonin, Eugene V},
  journal={Nucleic acids research},
  volume={43},
  number={D1},
  pages={D261--D269},
  year={2014},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383993/}
}

@article{emms2015orthofinder,
  title={OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
  author={Emms, David M and Kelly, Steven},
  journal={Genome biology},
  volume={16},
  number={1},
  pages={157},
  year={2015},
  publisher={BioMed Central},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531804/}
}


@article{krzywinski2009circos,
  title={Circos: An information aesthetic for comparative genomics},
  author={Krzywinski, Martin and Schein, Jacqueline and Birol, Inanç and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A},
  journal={Genome Research},
  volume={19},
  number={9},
  pages={1639},
  year={2009},
  publisher={Cold Spring Harbor Laboratory Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752132/}
}

@article{haft2017refseq,
  title={RefSeq: an update on prokaryotic genome annotation and curation},
  author={Haft, Daniel H and DiCuccio, Michael and Badretdin, Azat and Brover, Vyacheslav and Chetvernin, Vyacheslav and O’Neill, Kathleen and Li, Wenjun and Chitsaz, Farideh and Derbyshire, Myra K and Gonzales, Noreen R and others},
  journal={Nucleic acids research},
  volume={46},
  number={D1},
  pages={D851--D860},
  year={2017},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753331/}
}

@article{katoh2013mafft,
  title={MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
  author={Katoh, Kazutaka and Standley, Daron M},
  journal={Molecular biology and evolution},
  volume={30},
  number={4},
  pages={772--780},
  year={2013},
  publisher={Society for Molecular Biology and Evolution},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318/}
}

@article{price2010fasttree,
  title={FastTree 2--approximately maximum-likelihood trees for large alignments},
  author={Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P},
  journal={PloS one},
  volume={5},
  number={3},
  pages={e9490},
  year={2010},
  publisher={Public Library of Science},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/}
}

@article{federhen2011ncbi,
  title={The NCBI taxonomy database},
  author={Federhen, Scott},
  journal={Nucleic acids research},
  volume={40},
  number={D1},
  pages={D136--D143},
  year={2011},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245000/}
}


@article{kanehisa2019kegg,
  title={KEGG Mapper for inferring cellular functions from protein sequences},
  author={Kanehisa, Minoru and Sato, Yoko},
  journal={Protein Science},
  volume={-},
  number={-},
  pages={-},
  year={2019},
  publisher={Wiley Online Library},
  url={https://www.ncbi.nlm.nih.gov/pubmed/31423653}
}

@article{di2017nextflow,
  title={Nextflow enables reproducible computational workflows},
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  journal={Nature biotechnology},
  volume={35},
  number={4},
  pages={316},
  year={2017},
  publisher={Nature Publishing Group},
  url={https://www.ncbi.nlm.nih.gov/pubmed/28398311}
}
