Nature · 2015 · 1.4K citations · 36 references
AgriculturePlant BiologyPlant SciencesMetagenomicsMicrobial EcologyMicrobiome ResearchPlant MicrobiomePlant-associated Microbial CommunitiesRhizosphere InteractionsRhizosphere MicrobiologyRoot MicrobiomeRoot-microbe InteractionsMicrobial Colonization Of RootsPlant Microbiome DiversityRhizosphere MicrobiomesRoot-associated Bacterial CommunitiesRoot-associated Fungal CommunitiesRoot-associated Microbial CommunitiesRoot-microbiome Interactions
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Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa · Nucleic Acids Research · 2000 · 39.2K citations · Full text
KEGG: Kyoto Encyclopedia of Genes and Genomes
Hiroyuki Ogata, Susumu Goto, Kazushige Sato et al. · Nucleic Acids Research · 1999 · 32.4K citations · Full text
Prokka: rapid prokaryotic genome annotation
Torsten Seemann · Bioinformatics · 2014 · 19.6K citations
UPARSE: highly accurate OTU sequences from microbial amplicon reads
R. C. Edgar · Nature Methods · 2013 · 17.3K citations