An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion

Metagenomic sequencing of 706 longitudinally collected nasal swabs from infants with and without cystic fibrosis (CF) were used to construct and characterize a non-redundant gene catalog of the infant nasal microbiome. We aimed to determine how the infant nasal microbiome is perturbed by early therapies. Individual-assembly (build gene catalogue) pipeline_indAssembly.sh will run the assembly mapping_inddb.sh will map the reads to the gene catalogue eggnog.sh for functional annotation of the gene catalogue Analysis scripts euclidean_distances.cpp functions.R main.R will guide through the analysis Rsession.txt