microbiome R package
A reproducible nf-core/ampliseq pipeline characterizing antibiotic-mediated gut dysbiosis via paired-end 16S rRNA (V4) sequencing. Implements DADA2 exact sequence variant inference, SILVA-based taxonomic classification, and multivariate ecological ordination to quantify compositional perturbations in human fecal microbiomes.
Species-level pangenomes of the human oral microbiome constructed from eHOMD genomes using Anvi’o and reproducible Snakemake workflows.
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