Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines

Table 3

Summary of the main features of MG-RAST and QIIME.

	Availability	Analysis time	Prefiltering quality	16S rRNA detection mode	Taxonomic assignment methods*	Diversity analysis metrics§	Machine learning	Ease-of-use
MG-RAST	Web based	10 days (for private use)	Yes	Alignment with BLAT	One	One	No	Very simple; GUI
QIIME	Native code plus additional applications	2 hours	Yes	OTU-picking	Several	Several	Yes	Requires basic informatic skills; No GUI

GUI: Graphical user interface; *see Table 1; §see Table 2.