Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, Nicola, Waldron, Levi, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis·2012·Nature Methods

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  19. MetaGen: reference-free learning with multiple metagenomic samples
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