@article{Nayfach2019global_human_gut_microbiome, 
title={New insights from uncultivated genomes of the global human gut microbiome}, 
volume={568}, 
DOI={10.1038/s41586-019-1058-x}, 
number={7753}, 
journal={Nature}, 
author={Nayfach, 
Stephen and Shi, 
Zhou Jason and Seshadri, 
Rekha and Pollard, 
Katherine S. and Kyrpides, 
Nikos C.}, 
year={2019}, 
month={Mar}, 
pages={505–510} }


@article{Acinas_Sánchez_et_al_2021, 
title={Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities}, 
volume={4}, 
DOI={10.1038/s42003-021-02112-2}, 
number={1}, 
journal={Communications Biology}, 
author={Acinas, Silvia G. and Sánchez, Pablo and Salazar, Guillem and Cornejo-Castillo, Francisco M. and Sebastián, Marta and Logares, Ramiro and Royo-Llonch, Marta and Paoli, Lucas and Sunagawa, Shinichi and Hingamp, Pascal and Ogata, Hiroyuki and Lima-Mendez, Gipsi and Roux, Simon and González, José M. and Arrieta, Jesús M. and Alam, Intikhab S. and Kamau, Allan and Bowler, Chris and Raes, Jeroen and Pesant, Stéphane and Bork, Peer and Agustí, Susana and Gojobori, Takashi and Vaqué, Dolors and Sullivan, Matthew B. and Pedrós-Alió, Carlos and Massana, Ramon and Duarte, Carlos M. and Gasol, Josep M.}, 
year={2021}, 
month={May}, 
pages={1–15} }

@article{kang2019metabat,
  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},
  journal={PeerJ},
  volume={7},
  DOI={10.7717/peerj.7359},
  pages={e7359},
  year={2019},
  publisher={PeerJ Inc.}
}

@article{alneberg2014concoct,
  title={Binning metagenomic contigs by coverage and composition},
  author={Alneberg, Johannes and Bjarnason, Brynjar Sm{\'a}ri and De Bruijn, Ino and Schirmer, Melanie and Quick, Joshua and Ijaz, Umer Z and Lahti, Leo and Loman, Nicholas J and Andersson, Anders F and Quince, Christopher},
  journal={Nature methods},
  volume={11},
  DOI={10.1038/nmeth.3103},
  number={11},
  pages={1144--1146},
  year={2014},
  publisher={Nature Publishing Group US New York}
}


@article{nissen2021improved,
  title={Improved metagenome binning and assembly using deep variational autoencoders},
  author={Nissen, Jakob Nybo and Johansen, Joachim and Alles{\o}e, Rosa Lundbye and S{\o}nderby, Casper Kaae and Armenteros, Jose Juan Almagro and Gr{\o}nbech, Christopher Heje and Jensen, Lars Juhl and Nielsen, Henrik Bj{\o}rn and Petersen, Thomas Nordahl and Winther, Ole and others},
  journal={Nature biotechnology},
  volume={39},
  DOI={10.1038/s41587-020-00777-4},
  number={5},
  pages={555--560},
  year={2021},
  publisher={Nature Publishing Group US New York}
}


@article{sieber2018dastool,
  title={Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy},
  author={Sieber, Christian MK and Probst, Alexander J and Sharrar, Allison and Thomas, Brian C and Hess, Matthias and Tringe, Susannah G and Banfield, Jillian F},
  journal={Nature microbiology},
  volume={3},
  DOI={10.1038/s41564-018-0171-1},
  number={7},
  pages={836--843},
  year={2018},
  publisher={Nature Publishing Group UK London}
}


@article{ruhlemann2022magscot,
  title={MAGScoT: a fast, lightweight and accurate bin-refinement tool},
  author={R{\"u}hlemann, Malte Christoph and Wacker, Eike Matthias and Ellinghaus, David and Franke, Andre},
  journal={Bioinformatics},
  volume={38},
  DOI={10.1093/bioinformatics/btac694},
  number={24},
  pages={5430--5433},
  year={2022},
  publisher={Oxford University Press}
}

@article{uritskiy2018metawrap,
  title={MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis},
  author={Uritskiy, Gherman V and DiRuggiero, Jocelyne and Taylor, James},
  journal={Microbiome},
  volume={6},
  DOI={10.1186/s40168-018-0541-1},
  number={1},
  pages={1--13},
  year={2018},
  publisher={BioMed Central}
}

@article{meyer2022critical,
  title={Critical assessment of metagenome interpretation: the second round of challenges},
  author={Meyer, Fernando and Fritz, Adrian and Deng, Zhi-Luo and Koslicki, David and Lesker, Till Robin and Gurevich, Alexey and Robertson, Gary and Alser, Mohammed and Antipov, Dmitry and Beghini, Francesco and others},
  journal={Nature methods},
  volume={19},
  DOI={10.1038/s41592-022-01431-4},
  number={4},
  pages={429--440},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@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},
  DOI={10.1101/gr.186072.114},
  number={7},
  pages={1043--1055},
  year={2015},
  publisher={Cold Spring Harbor Lab}
}

@article{chklovski2023checkm2,
  title={CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning},
  author={Chklovski, Alex and Parks, Donovan H and Woodcroft, Ben J and Tyson, Gene W},
  journal={Nature Methods},
  volume={20},
  DOI={10.1038/s41592-023-01940-w},
  number={8},
  pages={1203--1212},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

@article{buchfink2015diamond,
  title={Fast and sensitive protein alignment using DIAMOND},
  author={Buchfink, Benjamin and Xie, Chao and Huson, Daniel H},
  journal={Nature methods},
  volume={12},
  DOI={10.1038/nmeth.3176},
  number={1},
  pages={59--60},
  year={2015},
  publisher={Nature Publishing Group US New York}
}

@article{larralde2022pyrodigal,
  title={Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes},
  author={Larralde, Martin},
  journal={Journal of Open Source Software},
  volume={7},
  DOI={10.21105/joss.04296},
  number={72},
  pages={4296},
  year={2022}
}

@article{hyatt2010prodigal,
  title={Prodigal: prokaryotic gene recognition and translation initiation site identification},
  author={Hyatt, Doug and Chen, Gwo-Liang and LoCascio, Philip F and Land, Miriam L and Larimer, Frank W and Hauser, Loren J},
  journal={BMC bioinformatics},
  volume={11},
  DOI={10.1186/1471-2105-11-119},
  pages={1--11},
  year={2010},
  publisher={Springer}
}



@article{metagWGS_inprep,
  title={MetagWGS, a complete workflow to analyse metagenomic data (from Illumina reads or PacBio HiFi reads)},
  author={Mainguy, Jean and Vienne, Maïna and Fourquet, Joanna and Darbot, Vincent and Noirot, Céline and Castinel, Adrien and Combes, Sylvie and Gaspin, Christine and Milan, Denis and Donnadieu, Cécile and Iampietro, Carole and Bouchez, Olivier and Pascal, Géraldine and Hoede, Claire}, 
  journal={Journal},
  year={in preparation}

}

