Extended Data Fig. 1: Overview of the study and metagenomic analysis pipeline. | Nature Medicine

Extended Data Fig. 1: Overview of the study and metagenomic analysis pipeline.

From: Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

Extended Data Fig. 1

a, Overview of the study. Fecal samples from 616 subjects were used to collect whole-genome shotgun sequencing data, from which functional and taxonomic profiles were generated. Fecal samples from 406 subjects were used to perform CE-TOFMS analysis to generate metabolite profiles. Samples from 347 subjects were available for both the sequencing and CE-TOFMS data analyses. KO, KEGG orthology. b, Flow chart of the pipeline used for the metagenomics analysis. Our metagenomics pipeline consists of three parts, quality control, functional profiling and taxonomic profiling, in which raw reads first undergo a quality control check and are then used to run several analytical steps to finally generate the KEGG orthology gene-based functional and taxonomic profiles.

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