Nature Methods, volume 17, issue 11, pages 1103-1110

metaFlye: scalable long-read metagenome assembly using repeat graphs.

Kolmogorov Mikhail ¹

Bickhart Derek M ²

Behsaz Bahar ³

Gurevich Alexey ⁴

Rayko Mike ⁴

Shin Sung Bong ⁵

Kuhn Kristen ⁵

Yuan Jeffrey ³

Polevikov Evgeny ^{4, 6}

Smith Timothy P. L. ⁵

Pevzner Pavel A. ^{1, 7}

Hide authors affiliations Show authors affiliations: 7 affiliations

Department of Computer Science and Engineering, University of California, San Diego, USA |

Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, USA |

Graduate Program in Bioinformatics and System Biology, University of California, San Diego, USA |

⁴

Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia |

⁵

USDA-ARS US Meat Animal Research Center, Clay Center, USA |

⁶

Bioinformatics Institute, St. Petersburg, Russia |

⁷

Center for Microbiome Innovation, University of California, San Diego, USA |

Publication type: Journal Article

Publication date: 2020-10-05

Springer Nature

Journal: Nature Methods

Quartile SCImago

Quartile WOS

Impact factor: 48

ISSN: 15487091, 15487105

DOI: 10.1038/s41592-020-00971-x

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Biochemistry

Molecular Biology

Cell Biology

Biotechnology

Abstract

Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products. Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

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Citations by journals

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Nature Biotechnology	Nature Biotechnology, 5, 1.22% Nature Biotechnology 5 publications, 1.22%
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Environmental Microbiology	Environmental Microbiology, 4, 0.98% Environmental Microbiology 4 publications, 0.98%
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Lecture Notes in Computer Science	Lecture Notes in Computer Science, 3, 0.73% Lecture Notes in Computer Science 3 publications, 0.73%
Applied and Environmental Microbiology	Applied and Environmental Microbiology, 3, 0.73% Applied and Environmental Microbiology 3 publications, 0.73%
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Frontiers in Plant Science	Frontiers in Plant Science, 2, 0.49% Frontiers in Plant Science 2 publications, 0.49%
Frontiers in Genetics	Frontiers in Genetics, 2, 0.49% Frontiers in Genetics 2 publications, 0.49%
	5 10 15 20 25

Citations by publishers

	10 20 30 40 50 60 70 80 90
Springer Nature	Springer Nature, 87, 21.27% Springer Nature 87 publications, 21.27%
American Society for Microbiology	American Society for Microbiology, 49, 11.98% American Society for Microbiology 49 publications, 11.98%
Frontiers Media S.A.	Frontiers Media S.A., 27, 6.6% Frontiers Media S.A. 27 publications, 6.6%
Elsevier	Elsevier, 25, 6.11% Elsevier 25 publications, 6.11%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 22, 5.38% Multidisciplinary Digital Publishing Institute (MDPI) 22 publications, 5.38%
Oxford University Press	Oxford University Press, 21, 5.13% Oxford University Press 21 publications, 5.13%
Wiley	Wiley, 14, 3.42% Wiley 14 publications, 3.42%
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Taylor & Francis	Taylor & Francis, 6, 1.47% Taylor & Francis 6 publications, 1.47%
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Mary Ann Liebert	Mary Ann Liebert, 2, 0.49% Mary Ann Liebert 2 publications, 0.49%
Han-Gug Misaengmul Hag-hoe/The Microbiological Society of Korea	Han-Gug Misaengmul Hag-hoe/The Microbiological Society of Korea, 2, 0.49% Han-Gug Misaengmul Hag-hoe/The Microbiological Society of Korea 2 publications, 0.49%
Genetics Society of America	Genetics Society of America, 2, 0.49% Genetics Society of America 2 publications, 0.49%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 2, 0.49% Cold Spring Harbor Laboratory 2 publications, 0.49%
Canadian Science Publishing	Canadian Science Publishing, 1, 0.24% Canadian Science Publishing 1 publication, 0.24%
PeerJ	PeerJ, 1, 0.24% PeerJ 1 publication, 0.24%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 1, 0.24% Public Library of Science (PLoS) 1 publication, 0.24%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 1, 0.24% American Society for Biochemistry and Molecular Biology 1 publication, 0.24%
IEEE	IEEE, 1, 0.24% IEEE 1 publication, 0.24%
American Society of Animal Science	American Society of Animal Science, 1, 0.24% American Society of Animal Science 1 publication, 0.24%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 1, 0.24% American Association for the Advancement of Science (AAAS) 1 publication, 0.24%
F1000 Research	F1000 Research, 1, 0.24% F1000 Research 1 publication, 0.24%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 1, 0.24% Proceedings of the National Academy of Sciences (PNAS) 1 publication, 0.24%
	10 20 30 40 50 60 70 80 90

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GOST Copy

Kolmogorov M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. // Nature Methods. 2020. Vol. 17. No. 11. pp. 1103-1110.

GOST all authors (up to 50) Copy

Kolmogorov M., Bickhart D. M., Behsaz B., Gurevich A., Rayko M., Shin S. B., Kuhn K., Yuan J., Polevikov E., Smith T. P. L., Pevzner P. A. metaFlye: scalable long-read metagenome assembly using repeat graphs. // Nature Methods. 2020. Vol. 17. No. 11. pp. 1103-1110.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1038/s41592-020-00971-x

UR - https://doi.org/10.1038%2Fs41592-020-00971-x

TI - metaFlye: scalable long-read metagenome assembly using repeat graphs.

T2 - Nature Methods

AU - Kolmogorov, Mikhail

AU - Bickhart, Derek M

AU - Behsaz, Bahar

AU - Gurevich, Alexey

AU - Rayko, Mike

AU - Shin, Sung Bong

AU - Kuhn, Kristen

AU - Yuan, Jeffrey

AU - Polevikov, Evgeny

AU - Smith, Timothy P. L.

AU - Pevzner, Pavel A.

PY - 2020

DA - 2020/10/05 00:00:00

PB - Springer Nature

SP - 1103-1110

IS - 11

VL - 17

SN - 1548-7091

SN - 1548-7105

ER -

BibTex |

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BibTex Copy

@article{2020_Kolmogorov,

author = {Mikhail Kolmogorov and Derek M Bickhart and Bahar Behsaz and Alexey Gurevich and Mike Rayko and Sung Bong Shin and Kristen Kuhn and Jeffrey Yuan and Evgeny Polevikov and Timothy P. L. Smith and Pavel A. Pevzner},

title = {metaFlye: scalable long-read metagenome assembly using repeat graphs.},

journal = {Nature Methods},

year = {2020},

volume = {17},

publisher = {Springer Nature},

month = {oct},

url = {https://doi.org/10.1038%2Fs41592-020-00971-x},

number = {11},

pages = {1103--1110},

doi = {10.1038/s41592-020-00971-x}

}

MLA

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MLA Copy

Kolmogorov, Mikhail, et al. “metaFlye: scalable long-read metagenome assembly using repeat graphs..” Nature Methods, vol. 17, no. 11, Oct. 2020, pp. 1103-1110. https://doi.org/10.1038%2Fs41592-020-00971-x.

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Springer Nature

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Nature Methods

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15487091 (Print)
15487105 (Electronic)