bio-workflows-microbiome-pipeline

To analyze 16S rRNA amplicon sequencing data, this pipeline processes paired-end FASTQ reads through DADA2 denoising, taxonomy assignment, and diversity testing to output ASV tables and differential abundance results.

Running differential abundance analysis on microbiome samples is best handled by integrating ALDEx2 with phyloseq objects to process taxonomic assignments and generate publication-ready results across multiple sample groups.

Yes, you can use DADA2 and phyloseq together for end-to-end amplicon analysis; this pipeline orchestrates DADA2 ASV inference and phyloseq diversity testing to produce taxonomic assignments and community structure figures.

To calculate alpha and beta diversity metrics across multiple sample groups, the pipeline applies phyloseq diversity analyses and PERMANOVA testing to evaluate community structure differences directly from denoised ASV tables.

Yes, this microbiome pipeline supports automated taxonomy assignment using reliable reference databases, processing denoised 16S reads to generate accurate taxonomic classifications for downstream diversity and differential abundance analyses.