Archives of Microbiology · 2019 · 94 citations · 27 references
Life SciencesBiologyMicrobiologyGenomicsMetagenomicsMicrobiome ResearchGut MicrobiomeGut MicrobiotaMetagenomic AnalysisMicrobial Community ProfilingShotgun Metagenomic SequencingShotgun MetagenomicsAntibiotic Resistance GenesAntibiotic Resistance ProfilingGut Microbiome DiversityMetagenomic Metabolic ReconstructionMicrobial MetagenomicsShotgun Metagenomic AnalysisShotgun Metagenomic ProfilingShotgun Sequencing
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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
Prokka: rapid prokaryotic genome annotation
Torsten Seemann · Bioinformatics · 2014 · 19.6K citations
Fast and sensitive protein alignment using DIAMOND
Benjamin Buchfink, Chao Xie, Daniel H. Huson · Nature Methods · 2014 · 15.2K citations
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt, Gwo-Liang Chen, Philip LoCascio et al. · BMC Bioinformatics · 2010 · 13.1K citations · Full text
Diet rapidly and reproducibly alters the human gut microbiome
Lawrence A. David, Corinne F. Maurice, Rachel N. Carmody et al. · Nature · 2013 · 10.2K citations · Full text