Functional Profiling

This step determines metabolic pathways of present microbial commnuties in gut microbiome. todo:read about metabolic pathways of gut microbial communities.

We will employ HUMAnN2 (Franzosa et al. 2018) for generating functional annotation of metagenomic data. This step utilises functional gene databases such as KEGG (Kyoto Encycolpedia of Genes and Genomes). The command below shows syntax for using HUMAnN2 for the task.

humann2 --input <input_file.fasta> --output <output_directory> --nucleotide-database /path/to/database

References

Franzosa, Eric A, Lauren J McIver, Gholamali Rahnavard, Luke R Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, et al. 2018. “Species-Level Functional Profiling of Metagenomes and Metatranscriptomes.” Nature Methods 15 (11): 962–68.