paper-refs.bib

@Book{Anderberg83,
   author =   {Anderberg, M. R.},
   title =    {Cluster Analysis for Applications},
   publisher =    {New York: Academic Press},
   year =     {1983},
 }

  @Manual{R:2010,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {Vienna, Austria: R Foundation for Statistical Computing},
    address = {},
    year = {2012},
    note = {{ISBN} 3-900051-07-0, http://www.R-project.org},
    url = {http://www.R-project.org},
  }

  @Manual{R:2008,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2008},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org},
  }

  @Article{Arabie80,
   author =   {Arabie, P. and Carroll, J. D.},
   title =    {MAPCLUS: A mathematical programming approach to fitting the ADCLUS models},
   journal =      {Psychometrika},
   year =     {1980 },
   volume =   {445},
   pages =    {211-35},
 }


@book{Tufte:1990,
	Address = {Cheshire, Connecticut},
	Author = {E. R. Tufte},
	Publisher = {Graphics Press},
	Title = {{Envisioning Information}},
	Year = {1990}}


@book{Tufte:1983,
	Address = {Cheshire},
	Author = {E. R. Tufte},
	Publisher = {Graphics Press},
	Title = {{The Visual Display of Quantitative Information}},
	Year = {1983}}

@book{Cleveland:1994,
	Address = {Summit},
	Author = {W. S. Cleveland},
	Edition = {Revised},
	Publisher = {Hobart Press},
	Title = {{The Elements of Graphing Data}},
	Year = {1994}}

@book{Cleveland:1993,
	Address = {Summit},
	Author = {W. S. Cleveland},
	Publisher = {Hobart Press},
	Title = {{Vizualizing Data}},
	Year = {1993}}

 @TECHREPORT{Ball65 ,
   AUTHOR =       {Ball, G. H. and Hall, D. J. },
   TITLE =        {A novel method of data analysis and pattern classification },
   INSTITUTION =  {Stanford Research Institute, California },
   YEAR =         {1965 },
 }

 @Article{Banfield93,
   author =   {Banfield, J. D. and Raftery, A. E.},
   title =    {Model-Based Gaussian and Non-Gaussian Clustering },
   journal =      {Biometrics },
   year =     {1993 },
   volume =   {49},
   pages =    {803--21},
 }

 @Article{Beale69,
   author =   {Beale, E. M. L.},
   title =    {Euclidean cluster analysis },
   journal =      {Bulletin of the International Statistical Institute },
   year =     {1969 },
   volume =   {43},
   pages =    {92-94},
 }

 @Article{Bensmail,
   author =   {Bensmail, H. },
   title =    {Model-based Clustering with Noise: Bayesian inference and estimation },
 }

@Article{Bezdek74,
   author =   {Bezdek, J. C.},
   title =    {Numerical taxonomy with fuzzy sets},
   journal =      {Journal of Mathematical Biology},
   year =     {1974},
   volume =   {1},
   pages =    {57-71},
 }

@article{Cox:1972,
	Author = {D. R. Cox},
	Journal = {J. R. Statist. Soc. {\rm B}},
	Pages = {187--220},
	Title = {{Regression models and life tables (with Discussion)}},
	Volume = {34},
	Year = {1972}}

@article{Hear:Holm:Step:quan:2006,
	Author = {Heard, Nicholas A. and Holmes, Christopher C. and Stephens, David A.},
	Journal = {J. Am. Statist. Assoc.},
	Keywords = {bayesian hierarchical clustering; gene expression profiles; Microarrays},
	Pages = {18--29},
	Title = {A Quantitative Study of Gene Regulation Involved in the Immune Response of {A}nopheline Mosquitoes: {A}n Application of {B}ayesian Hierarchical Clustering of Curves},
	Volume = {101},
	Year = {2006}}

@article{Fan:2004,
	Author = {Fan, J. and Peng, H.},
	Journal = {Ann. Statist.},
	Pages = {928--61},
	Title = {{Nonconcave penalized likelihood with a diverging number of parameters}},
	Volume = {32},
	Year = {2004}}
    
@article{rook2017evolution,
  title={Evolution, human-microbe interactions, and life history plasticity},
  author={Rook, Graham and B{\"a}ckhed, Fredrik and Levin, Bruce R and McFall-Ngai, Margaret J and McLean, Angela R},
  journal={The Lancet},
  volume={390},
  number={10093},
  pages={521--530},
  year={2017},
  publisher={Elsevier}
}

@article{rubino2017divergent,
  title={Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome},
  author={Rubino, Francesco and Carberry, Ciara and Waters, Sin{\'e}ad M and Kenny, David and McCabe, Matthew S and Creevey, Christopher J},
  journal={The ISME journal},
  volume={11},
  number={4},
  pages={932},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{quince2017shotgun,
  title={Shotgun metagenomics, from sampling to analysis},
  author={Quince, Christopher and Walker, Alan W and Simpson, Jared T and Loman, Nicholas J and Segata, Nicola},
  journal={Nature biotechnology},
  volume={35},
  number={9},
  pages={833},
  year={2017},
  publisher={Nature Publishing Group}
}

@misc{marx2016microbiology,
  title={Microbiology: the road to strain-level identification},
  author={Marx, Vivien},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{quince2017desman,
  title={DESMAN: a new tool for de novo extraction of strains from metagenomes},
  author={Quince, Christopher and Delmont, Tom O and Raguideau, S{\'e}bastien and Alneberg, Johannes and Darling, Aaron E and Collins, Gavin and Eren, A Murat},
  journal={Genome biology},
  volume={18},
  number={1},
  pages={181},
  year={2017},
  publisher={BioMed Central}
}

@article{sczyrba2017critical,
  title={Critical assessment of metagenome interpretation—a benchmark of metagenomics software},
  author={Sczyrba, Alexander and Hofmann, Peter and Belmann, Peter and Koslicki, David and Janssen, Stefan and Dr{\"o}ge, Johannes and Gregor, Ivan and Majda, Stephan and Fiedler, Jessika and Dahms, Eik and others},
  journal={Nature Methods},
  volume={14},
  number={11},
  pages={1063},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{li2018minimap2,
  title={Minimap2: pairwise alignment for nucleotide sequences},
  author={Li, Heng},
  journal={Bioinformatics},
  volume={1},
  pages={7},
  year={2018},
  publisher={Oxford University Press}
}

@article{li2016minimap,
  title={Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
  author={Li, Heng},
  journal={Bioinformatics},
  volume={32},
  number={14},
  pages={2103--2110},
  year={2016},
  publisher={Oxford University Press}
}



% Generated by Paperpile. Check out http://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.

@ARTICLE{Mason2017-yj,
  title     = "{International Standards for Genomes, Transcriptomes, and
               Metagenomes}",
  author    = "Mason, Christopher E and Afshinnekoo, Ebrahim and Tighe, Scott
               and Wu, Shixiu and Levy, Shawn",
  journal   = "Journal of Biomolecular Techniques",
  publisher = "ncbi.nlm.nih.gov",
  volume    =  28,
  number    =  1,
  pages     = "8--18",
  month     =  apr,
  year      =  2017,
  keywords  = "epigenomics; epitranscriptomics; genomics; metagenomics;
               transcriptomics",
  language  = "en",
  issn      = "1524-0215, 1943-4731",
  pmid      = "28337071",
  doi       = "10.7171/jbt.17-2801-006",
  pmc       = "PMC5359768"
}

@ARTICLE{Payne2018-cv,
author = {Payne, Alexander and Holmes, Nadine and Rakyan, Vardhman and Loose, Matthew},                                              
title = {BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files},                                                          
journal = {Bioinformatics},                                       
volume = {},                                                      
number = {},                                                      
pages = {bty841},                                                 
year = {2018},                                                    
doi = {10.1093/bioinformatics/bty841},                            
}

@ARTICLE{Bertrand2018-lz,
        author = {Bertrand, Denis and Shaw, Jim and Narayan, Manesh and Ng, Hui Qi Amanda and Kumar, Senthil and Li, Chenhao and Dvornicic, Mirta and Paliska Soldo, Janja and Kho, Jia Yu and Ng, Oon Tek and Barkham, Timothy and Young, Barnaby and Marimuthu, Kalisvar and Chng, Kern Rei and Sikic, Mile and Nagarajan, Niranjan},     
        title = {Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome},                                                                                                                        
        year = {2018},                                            
        doi = {10.1101/456905},                                   
        publisher = {Cold Spring Harbor Laboratory},
  journal   = "bioRxiv",
  pages = {456905},
}
@ARTICLE{Jain2018-aw,
  title     = "{Nanopore sequencing and assembly of a human genome with
               ultra-long reads}",
  author    = "Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh
               and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and
               Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and
               Malla, Sunir and Marriott, Hannah and Nieto, Tom and O'Grady,
               Justin and Olsen, Hugh E and Pedersen, Brent S and Rhie, Arang
               and Richardson, Hollian and Quinlan, Aaron R and Snutch,
               Terrance P and Tee, Louise and Paten, Benedict and Phillippy,
               Adam M and Simpson, Jared T and Loman, Nicholas J and Loose,
               Matthew",
  journal   = "Nature Biotechnology",
  publisher = "The Author(s)",
  volume    =  36,
  pages     = "338",
  month     =  jan,
  year      =  2018,
  keywords  = "mypubs",
  issn      = "1087-0156",
  doi       = "10.1038/nbt.4060"
}

% Generated by Paperpile. Check out http://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.

@ARTICLE{Huson2007-mk,
  title    = "{MEGAN analysis of metagenomic data}",
  author   = "Huson, Daniel H and Auch, Alexander F and Qi, Ji and Schuster,
              Stephan C",
  journal  = "Genome Research",
  volume   =  17,
  number   =  3,
  pages    = "377--386",
  month    =  mar,
  year     =  2007,
  language = "en",
  issn     = "1088-9051",
  pmid     = "17255551",
  doi      = "10.1101/gr.5969107",
  pmc      = "PMC1800929"
}

@ARTICLE{Leggett2017-sx,
        author = {Leggett, Richard M. and Alcon-Giner, Cristina and Heavens, Darren and Caim, Shabhonam and Brook, Thomas C. and Kujawska, Magdalena and Martin, Samuel and Hoyles, Lesley and Clarke, Paul and Hall, Lindsay and Clark, Matthew D.},
        title = {Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics},
        year = {2018},
        doi = {10.1101/180406},
        publisher = {Cold Spring Harbor Laboratory},

  journal   = "bioRxiv",
  pages = {180406}

}

@ARTICLE{Somerville2018-mq,
        author = {Somerville, Vincent and Lutz, Stefanie and Schmid, Michael and Frei, Daniel and Moser, Aline and Irmler, Stefan and Frey, Juerg E. and Ahrens, Christian H.},
        title = {Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system},
        year = {2018},
        doi = {10.1101/476747},
        publisher = {Cold Spring Harbor Laboratory},
  journal   = "bioRxiv",

  pages = {476747}
}

@ARTICLE{Ackelsberg2015-fh,
  title    = "{Lack of Evidence for Plague or Anthrax on the New York City
              Subway}",
  author   = "Ackelsberg, Joel and Rakeman, Jennifer and Hughes, Scott and
              Petersen, Jeannine and Mead, Paul and Schriefer, Martin and
              Kingry, Luke and Hoffmaster, Alex and Gee, Jay E",
  journal  = "Cell Systems",
  volume   =  1,
  number   =  1,
  pages    = "4--5",
  month    =  jul,
  year     =  2015,
  language = "en",
  issn     = "2405-4712",
  pmid     = "27135683",
  doi      = "10.1016/j.cels.2015.07.008"
}

@ARTICLE{Hug2016-wz,
  title     = "{A new view of the tree of life}",
  author    = "Hug, Laura A and Baker, Brett J and Anantharaman, Karthik and
               Brown, Christopher T and Probst, Alexander J and Castelle, Cindy
               J and Butterfield, Cristina N and Hernsdorf, Alex W and Amano,
               Yuki and Ise, Kotaro and Suzuki, Yohey and Dudek, Natasha and
               Relman, David A and Finstad, Kari M and Amundson, Ronald and
               Thomas, Brian C and Banfield, Jillian F",
  journal   = "Nature Microbiology",
  publisher = "nature.com",
  volume    =  1,
  pages     = "16048",
  month     =  apr,
  year      =  2016,
  language  = "en",
  issn      = "2058-5276",
  pmid      = "27572647",
  doi       = "10.1038/nmicrobiol.2016.48"
}


@ARTICLE{Sanderson2018-zf,
  title    = "{Real-time analysis of nanopore-based metagenomic sequencing from
              infected orthopaedic devices}",
  author   = "Sanderson, Nicholas D and Street, Teresa L and Foster, Dona and
              Swann, Jeremy and Atkins, Bridget L and Brent, Andrew J and
              McNally, Martin A and Oakley, Sarah and Taylor, Adrian and Peto,
              Tim E A and Crook, Derrick W and Eyre, David W",
  journal  = "BMC Genomics",
  volume   =  19,
  number   =  1,
  pages    = "714",
  month    =  sep,
  year     =  2018,
  keywords = "Clinical; Device-related infection; Metagenomics; Nanopore;
              Prosthetic joint infection; Real-time",
  language = "en",
  issn     = "1471-2164",
  pmid     = "30261842",
  doi      = "10.1186/s12864-018-5094-y",
  pmc      = "PMC6161345"
}

@ARTICLE{Simpson2017-gn,
  title    = "{Detecting DNA cytosine methylation using nanopore sequencing}",
  author   = "Simpson, Jared T and Workman, Rachael E and Zuzarte, P C and
              David, Matei and Dursi, L J and Timp, Winston",
  journal  = "Nature Methods",
  volume   =  14,
  number   =  4,
  pages    = "407--410",
  month    =  apr,
  year     =  2017,
  language = "en",
  issn     = "1548-7091, 1548-7105",
  pmid     = "28218898",
  doi      = "10.1038/nmeth.4184"
}

@ARTICLE{Charalampous2018-fl,
        author = {Charalampous, Themoula and Richardson, Hollian and Kay, Gemma Louise and Baldan, Rossella and Jeanes, Christopher and Rae, Duncan and Grundy, Sara and Turner, Daniel J and Wain, John and Leggett, Richard Mark and Livermore, David M and O{\textquoteright}Grady, Justin},
        title = {Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics},
        year = {2018},
        doi = {10.1101/387548},
        publisher = {Cold Spring Harbor Laboratory},

  journal   = "bioRxiv",
  pages = {387548}
}

@ARTICLE{Wommack2008-qf,
  title    = "{Metagenomics: read length matters}",
  author   = "Wommack, K Eric and Bhavsar, Jaysheel and Ravel, Jacques",
  journal  = "Applied and Environmental Microbiology",
  volume   =  74,
  number   =  5,
  pages    = "1453--1463",
  month    =  mar,
  year     =  2008,
  language = "en",
  issn     = "0099-2240, 1098-5336",
  pmid     = "18192407",
  doi      = "10.1128/AEM.02181-07",
  pmc      = "PMC2258652"
}



@ARTICLE{Bankevich2012-iu,
  title     = "{SPAdes: a new genome assembly algorithm and its applications to
               single-cell sequencing}",
  author    = "Bankevich, Anton and Nurk, Sergey and Antipov, Dmitry and
               Gurevich, Alexey A and Dvorkin, Mikhail and Kulikov, Alexander S
               and Lesin, Valery M and Nikolenko, Sergey I and Pham, Son and
               Prjibelski, Andrey D and Pyshkin, Alexey V and Sirotkin,
               Alexander V and Vyahhi, Nikolay and Tesler, Glenn and Alekseyev,
               Max A and Pevzner, Pavel A",
  journal   = "Journal of Computational Biology",
  publisher = "online.liebertpub.com",
  volume    =  19,
  number    =  5,
  pages     = "455--477",
  month     =  may,
  year      =  2012,
  language  = "en",
  issn      = "1066-5277, 1557-8666",
  pmid      = "22506599",
  doi       = "10.1089/cmb.2012.0021",
  pmc       = "PMC3342519"
}


@ARTICLE{Handelsman2004-lg,
  title     = "{Metagenomics: application of genomics to uncultured
               microorganisms}",
  author    = "Handelsman, Jo",
  journal   = "Microbiology and Molecular Biology Reviews",
  publisher = "Am Soc Microbiol",
  volume    =  68,
  number    =  4,
  pages     = "669--685",
  month     =  dec,
  year      =  2004,
  language  = "en",
  issn      = "1092-2172",
  pmid      = "15590779",
  doi       = "10.1128/MMBR.68.4.669-685.2004",
  pmc       = "PMC539003"
}

@article{li2009sequence,
  title={The sequence alignment/map format and SAMtools},
  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},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2078--2079},
  year={2009},
  publisher={Oxford University Press}
}


@ARTICLE{Rang2018-md,
  title    = "{From squiggle to basepair: computational approaches for improving
              nanopore sequencing read accuracy}",
  author   = "Rang, Franka J and Kloosterman, Wigard P and de Ridder, Jeroen",
  journal  = "Genome Biology",
  volume   =  19,
  number   =  1,
  pages    = "90",
  month    =  jul,
  year     =  2018,
  language = "en",
  issn     = "1465-6906",
  pmid     = "30005597",
  doi      = "10.1186/s13059-018-1462-9",
  pmc      = "PMC6045860"
}

@ARTICLE{Huson2018-bh,
  title     = "{MEGAN-LR: new algorithms allow accurate binning and easy
               interactive exploration of metagenomic long reads and contigs}",
  author    = "Huson, Daniel H and Albrecht, Benjamin and Bağcı, Caner and
               Bessarab, Irina and Górska, Anna and Jolic, Dino and Williams,
               Rohan B H",
  journal   = "Biology Direct",
  publisher = "biologydirect.biomedcentral.com",
  volume    =  13,
  number    =  1,
  pages     = "6",
  month     =  apr,
  year      =  2018,
  keywords  = "Algorithms; Functional binning; Long reads; Microbiome;
               Nanopore; PacBio; Sequence analysis; Software; Taxonomic binning",
  language  = "en",
  issn      = "1745-6150",
  pmid      = "29678199",
  doi       = "10.1186/s13062-018-0208-7",
  pmc       = "PMC5910613"
}

@ARTICLE{Quince2017-lf,
  title    = "{Shotgun metagenomics, from sampling to analysis}",
  author   = "Quince, Christopher and Walker, Alan W and Simpson, Jared T and
              Loman, Nicholas J and Segata, Nicola",
  journal  = "Nature Biotechnology",
  volume   =  35,
  number   =  9,
  pages    = "833--844",
  month    =  sep,
  year     =  2017,
  language = "en",
  issn     = "1087-0156, 1546-1696",
  pmid     = "28898207",
  doi      = "10.1038/nbt.3935"
}


@Article{Wood2014,                                                
author="Wood, Derrick E.                                          
and Salzberg, Steven L.",                                         
title="Kraken: ultrafast metagenomic sequence classification using exact alignments",                                                
journal="Genome Biology",                                         
year="2014",                                                      
month="Mar",                                                      
day="03",                                                         
volume="15",                                                      
number="3",                                                       
pages="R46",                                                      
abstract="Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.",                                                                           
issn="1474-760X",                                                 
doi="10.1186/gb-2014-15-3-r46",                                   
                 
}  


@ARTICLE{Quick2014-sj,
  title    = "{A reference bacterial genome dataset generated on the MinION™
              portable single-molecule nanopore sequencer}",
  author   = "Quick, Joshua and Quinlan, Aaron R and Loman, Nicholas J",
  journal  = {GigaScience},
  volume   =  3,
  pages    = "22",
  month    =  oct,
  year     =  2014,
  keywords = "Genomics; Nanopore sequencing",
  language = "en",
  issn     = "2047-217X",
  pmid     = "25386338",
  doi      = "10.1186/2047-217X-3-22",
  pmc      = "PMC4226419"
}

@article{vaser2017fast,
  title={Fast and accurate de novo genome assembly from long uncorrected reads},
  author={Vaser, Robert and Sovi{\'c}, Ivan and Nagarajan, Niranjan and {\v{S}}iki{\'c}, Mile},
  journal={Genome Research},
  volume={27},
  number={5},
  pages={737--746},
  year={2017},
  publisher={Cold Spring Harbor Lab}
}

@article{walker2014pilon,
  title={Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement},
  author={Walker, Bruce J and Abeel, Thomas and Shea, Terrance and Priest, Margaret and Abouelliel, Amr and Sakthikumar, Sharadha and Cuomo, Christina A and Zeng, Qiandong and Wortman, Jennifer and Young, Sarah K and others},
  journal={PloS One},
  volume={9},
  number={11},
  pages={e112963},
  year={2014},
  publisher={Public Library of Science}
}

@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}
}

@article{mcintyre2019single,
  title={Single-molecule sequencing detection of N 6-methyladenine in microbial reference materials},
  author={McIntyre, Alexa BR and Alexander, Noah and Grigorev, Kirill and Bezdan, Daniela and Sichtig, Heike and Chiu, Charles Y and Mason, Christopher E},
  journal={Nature Communications},
  volume={10},
  number={1},
  pages={579},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{chin2013nonhybrid,
  title={Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data},
  author={Chin, Chen-Shan and Alexander, David H and Marks, Patrick and Klammer, Aaron A and Drake, James and Heiner, Cheryl and Clum, Alicia and Copeland, Alex and Huddleston, John and Eichler, Evan E and others},
  journal={Nature Methods},
  volume={10},
  number={6},
  pages={563},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{koster2012snakemake,
  title={Snakemake—a scalable bioinformatics workflow engine},
  author={K{\"o}ster, Johannes and Rahmann, Sven},
  journal={Bioinformatics},
  volume={28},
  number={19},
  pages={2520--2522},
  year={2012},
  publisher={Oxford University Press}
}

@article{ruan2019fast,
  title={Fast and accurate long-read assembly with wtdbg2},
  author={Ruan, Jue and Li, Heng},
  journal={BioRxiv},
  pages={530972},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{mcintyre2017comprehensive,
  title={Comprehensive benchmarking and ensemble approaches for metagenomic classifiers},
  author={McIntyre, Alexa BR and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and others},
  journal={Genome biology},
  volume={18},
  number={1},
  pages={182},
  year={2017},
  publisher={BioMed Central}
}