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.
nextflow bioinformatics-pipeline antibiotic-resistance microbiome-analysis human-microbiome microbial-ecology dada2 gut-microbiome amplicon-sequencing bacteriology bifidobacterium 16s-rrna nf-core dysbiosis microbial-diversity
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Updated
May 1, 2026 - Python