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Fast and sensitive taxonomic classification for metagenomics with Kaiju

Citations

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Cited by:

  1. Daniela S. Aliaga Goltsman & Lisa M. Alexander & Jyun-Liang Lin & Rodrigo Fregoso Ocampo & Benjamin Freeman & Rebecca C. Lamothe & Andres Perez Rivas & Morayma M. Temoche-Diaz & Shailaja Chadha & Nata, 2022. "Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  2. Louise B. Sennett & Constance A. Roco & Natalie Y. N. Lim & Joseph B. Yavitt & Peter Dörsch & Lars R. Bakken & James P. Shapleigh & Åsa Frostegård, 2024. "Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  3. Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  4. Na Zhou & Qihao Li & Zhiwei Liang & Ke Yu & Chunfang Zhang & Huijuan Wang & Pengcheng Li & Zhili He & Shanquan Wang, 2025. "Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  5. Cong Wang & Qing-Yi Yu & Niu-Niu Ji & Yong Zheng & John W. Taylor & Liang-Dong Guo & Cheng Gao, 2023. "Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  6. Manoshi S. Datta & Idan Yelin & Ori Hochwald & Imad Kassis & Liron Borenstein-Levin & Amir Kugelman & Roy Kishony, 2021. "Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
  7. Peng Liu & Jessica Ewald & Zhiqiang Pang & Elena Legrand & Yeon Seon Jeon & Jonathan Sangiovanni & Orcun Hacariz & Guangyan Zhou & Jessica A. Head & Niladri Basu & Jianguo Xia, 2023. "ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  8. Aiswarya Prasad & Asha D. Pallujam & Rajath Siddaganga & Ashwin Suryanarayanan & Florent Mazel & Axel Brockmann & Sze H. Yek & Philipp Engel, 2025. "Evolution of gut microbiota across honeybee species revealed by comparative metagenomics," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  9. J. L. Rolando & M. Kolton & T. Song & Y. Liu & P. Pinamang & R. Conrad & J. T. Morris & K. T. Konstantinidis & J. E. Kostka, 2024. "Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  10. Jason Liu & Daniela S. Aliaga Goltsman & Lisa M. Alexander & Khak Khak Khayi & Jennifer H. Hong & Drew T. Dunham & Christine A. Romano & Morayma M. Temoche-Diaz & Shailaja Chadha & Rodrigo Fregoso Oca, 2025. "Integration of therapeutic cargo into the human genome with programmable type V-K CAST," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  11. Omary Mzava & Alexandre Pellan Cheng & Adrienne Chang & Sami Smalling & Liz-Audrey Kounatse Djomnang & Joan Sesing Lenz & Randy Longman & Amy Steadman & Luis G. Gómez-Escobar & Edward J. Schenck & Mir, 2022. "A metagenomic DNA sequencing assay that is robust against environmental DNA contamination," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  12. Dutta, Arup & Barbora, Lepakshi & Stom, Devard & Goswami, Pranab, 2025. "Improving power performance of sediment microbial fuel cell through Water lettuce (Pistia stratiotes) assisted boosting of cathodic activity," Renewable and Sustainable Energy Reviews, Elsevier, vol. 215(C).
  13. Márk Szuhaj & Roland Wirth & Zoltán Bagi & Gergely Maróti & Gábor Rákhely & Kornél L. Kovács, 2021. "Development of Stable Mixed Microbiota for High Yield Power to Methane Conversion," Energies, MDPI, vol. 14(21), pages 1-17, November.
  14. Nancy O. Nou & Jonathan K. Covington & Dengxun Lai & Xavier Mayali & Cale O. Seymour & Juliet Johnston & Jian-Yu Jiao & Steffen Buessecker & Damon Mosier & Alise R. Muok & Nicole Torosian & Allison M., 2024. "Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  15. Amanda Sörensen Ristinmaa & Albert Tafur Rangel & Alexander Idström & Sebastian Valenzuela & Eduard J. Kerkhoven & Phillip B. Pope & Merima Hasani & Johan Larsbrink, 2023. "Resin acids play key roles in shaping microbial communities during degradation of spruce bark," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  16. Heleen T. Ouboter & Rob Mesman & Tom Sleutels & Jelle Postma & Martijn Wissink & Mike S. M. Jetten & Annemiek Ter Heijne & Tom Berben & Cornelia U. Welte, 2024. "Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  17. Mason. R. Stothart & Philip. D. McLoughlin & Sarah. A. Medill & Ruth. J. Greuel & Alastair. J. Wilson & Jocelyn. Poissant, 2024. "Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  18. Zheng Sun & Jiang Liu & Meng Zhang & Tong Wang & Shi Huang & Scott T. Weiss & Yang-Yu Liu, 2023. "Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  19. Kaiyuan Zhu & Alejandro A. Schäffer & Welles Robinson & Junyan Xu & Eytan Ruppin & A. Funda Ergun & Yuzhen Ye & S. Cenk Sahinalp, 2022. "Strain level microbial detection and quantification with applications to single cell metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  20. Marc Schoeler & Sandrine Ellero-Simatos & Till Birkner & Jordi Mayneris-Perxachs & Lisa Olsson & Harald Brolin & Ulrike Loeber & Jamie D. Kraft & Arnaud Polizzi & Marian Martí-Navas & Josep Puig & Ant, 2023. "The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  21. Lingrui Kong & Yiming Feng & Ru Zheng & Xiaogang Wu & Yimin Mao & Jingqi Sun & Sitong Liu, 2025. "Interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria drives nitrogen loss," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  22. Harold P. Hodgins & Pengsheng Chen & Briallen Lobb & Xin Wei & Benjamin J. M. Tremblay & Michael J. Mansfield & Victoria C. Y. Lee & Pyung-Gang Lee & Jeffrey Coffin & Ana T. Duggan & Alexis E. Dolphin, 2023. "Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  23. Danijel Jovicic & Konstantinos Anestis & Jacek Fiutowski & Bo Barker Jørgensen & Kasper Urup Kjeldsen & Amelia-Elena Rotaru, 2026. "Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments," Nature Communications, Nature, vol. 17(1), pages 1-14, December.
  24. Lharbi Dridi & Fernando Altamura & Emmanuel Gonzalez & Olivia Lui & Ryszard Kubinski & Reilly Pidgeon & Adrian Montagut & Jasmine Chong & Jianguo Xia & Corinne F. Maurice & Bastien Castagner, 2023. "Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  25. Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  26. Alexa M. Nicolas & Ella T. Sieradzki & Jennifer Pett-Ridge & Jillian F. Banfield & Michiko E. Taga & Mary K. Firestone & Steven J. Blazewicz, 2023. "A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
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