CBW workshop 2024 advanced - LangilleLab/microbiome_helper GitHub Wiki

This page is currently a work in progress. It will contain information about the 2024 CBW Advanced Microbiome Analysis: St John's, NL

Module 1: Introduction to metagenomics and read-based profiling

• Quality control of short reads and removal of host contamination using Kneaddata in the Unix command line
• Taxonomic profiling of short reads using Kraken and MetaPhlAn in the Unix command line
• Analysis of taxonomic assignment results using Phyloseq in R

Module 2: Metagenomic Assembly and Binning

• Assembly of short reads into contigs, binning of contigs and refinement of bins into Metagenome Assembled Genomes (MAGs) using Anv’io in the Unix command line
• Metrics for assessing MAG quality using Anv’io in the Unix command line

Module 3: Metagenomic functional annotation

• General functional annotation using MMSeqs and HUMAnN in the Unix command line
• AMR annotation of reads using CARD RGI in the Unix command line
• Visualization of functions stratified by taxonomy using JarrVis in R

Module 4: Advanced microbiome statistics

• Statistics and machine learning in R