External Resources

Analysis pipelines and tutorials

• QIIME2 documentation — tutorials, plugin references, and a community forum for the most widely used microbiome analysis platform
• nf-core/ampliseq — a Nextflow pipeline for amplicon sequencing analysis maintained by the nf-core community
• DADA2 tutorial — R-based ASV pipeline
• phyloseq tutorials — R package for microbiome data analysis and visualization
• National Microbiome Data Collaborative Microbiome Scence Certificate Program — Overarching, in-depth overview of microbiome analyses free for public

Reference databases and comparative datasets

• Earth Microbiome Project — protocols, reference databases, and comparative datasets
• Silva database — rRNA reference database for taxonomy assignment
• Greengenes2 — updated 16S reference database