@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},
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  number={1},
  pages={59--60},
  year={2015},
  publisher={Nature Publishing Group US New York}
}

@article{larralde2022pyrodigal,
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  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},
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  DOI={10.1186/1471-2105-11-119},
  pages={1--11},
  year={2010},
  publisher={Springer}
}


@article {metagWGS,
	author = {Mainguy, Jean and Vienne, M{\"a}ina and Fourquet, Joanna and Darbot, Vincent and Noirot, C{\'e}line and Castinel, Adrien and Combes, Sylvie and Gaspin, Christine and Milan, Denis and Donnadieu, Cecile and Iampietro, Carole and Bouchez, Olivier and Pascal, G{\'e}raldine and Hoede, Claire},
	title = {metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads},
	elocation-id = {2024.09.13.612854},
	year = {2024},
	doi = {10.1101/2024.09.13.612854},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Background: To study communities of micro-organisms taxonomically and functionally, metagenomic analyses are now often used. If there is no reference gene catalogue, a de novo approach is required. Because genomes are easier to interpret than contigs, the recovery of metagenome-assembled genomes (MAGs) by binning of contigs from metagenomic data has recently become a common task for microbial studies. However, during this process, there is a significant loss of information between the assembly and the binning of contigs. This is why it is important to produce taxonomic and functional matrices for all contigs and not just those included in correct bins. In addition, Pacbio HiFi reads (long and of good quality) are now a possible, albeit more expensive, alternative to short Illumina reads. We therefore developed a workflow that is easy to install with dependencies fixed using singularity images and easy to use on a computing cluster, that is capable of analyzing either short or long reads, and that should allow analysis at the contig and/or bin level, depending on the user{\textquoteright}s choice. Following is a presentation of metagWGS, a fully automated workflow for metagenomic data analysis. It uses a new tool for refining bins (called Binette) that we will demonstrate is more efficient than competing tools. Methods: metagWGS is a Nextflow workflow distributed with two singularity images and complete documentation to facilitate its installation and use. Because the main original features of metagWGS concern binning (short and long reads) and the analysis of HiFi reads, we compared metagWGS with the MAG construction workflow proposed by PacBio to a public dataset used by Pacbio to promote its workflow. Results: metagWGS differs from existing workflows by (i) offering flexible approaches for the assembly; (ii) supporting short reads (Illumina) or PacBio HiFi reads; (iii) combining multiple binning algorithms with a new bin refinement tool, referred to as Binette, to achieve high-quality genome bins; and (iv) providing taxonomic and functional annotation for all genes, all contigs built and bins. metagWGS produces more medium (708) and high-quality (255) bins on 11 public metagenomic samples from human gut data than the Pacbio HiFi dedicated workflow, referred to as the HiFi-MAGS-pipeline (659 medium quality bins and 231 high quality bins), primarily due to the better performance of Binette.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2024/09/18/2024.09.13.612854},
	eprint = {https://www.biorxiv.org/content/early/2024/09/18/2024.09.13.612854.full.pdf},
	journal = {bioRxiv}
}


@article{gruning2018bioconda,
  title={Bioconda: sustainable and comprehensive software distribution for the life sciences},
  author={Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A and Rowe, Jillian and Tomkins-Tinch, Christopher H and Valieris, Renan and K{\"o}ster, Johannes and Bioconda Team},
  journal={Nature methods},
  volume={15},
  number={7},
  pages={475--476},
  year={2018},
  publisher={Nature Publishing Group US New York},
  doi = {10.1038/s41592-018-0046-7},
}


@article{Bioconda:2018,
  title = {Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences},
  shorttitle = {Bioconda},
  author = {Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A. and Rowe, Jillian and {Tomkins-Tinch}, Christopher H. and Valieris, Renan and K{\"o}ster, Johannes},
  year = {2018},
  month = jul,
  journal = {Nature Methods},
  volume = {15},
  number = {7},
  pages = {475--476},
  publisher = {{Nature Publishing Group}},
  issn = {1548-7105},
  doi = {10.1038/s41592-018-0046-7},
}

