Tutorial for analysis of 16S rRNA gene amplicon data

Our laboratory’s tutorial and walk-through for analysis of 16S rRNA gene amplicon data

This tutorial was developed by Chris Brown and presented at the 2021 American Thoracic Society Post-Graduate Course: “A Hands-On Introduction to Studying the Lung Microbiome.” Data and source code available at the link; data are from this study.

Droplet Digital PCR

Protocol for absolute quantification of the bacterial 16S rRNA gene using droplet digital PCR (BioRad)

GitHub

Dickson Laboratory GitHub site

Software packages

SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data (manuscript, software)

AMAISE: a machine learning approach to index-free sequence enrichment (manuscript, software)