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BioBakery

Training materials for a short BioBakery workshop organised at the Quadram Institute Bioscience in June 2024.

• Datasets - public datasets you can download and analyse yourself

Running Metaphlan4 and Humann3

• Human reads removal - removing human reads
• MetaPhlAn - taxonomic classification of reads using clade-specific markers
• HuMANN - functional profiling of metagenomics reads

Executing

• Running bioBakery tools from the HPC
• Running bioBakery tools from your QIB VM
• nf-core/taxprofiler - a standardised pipeline to run multiple profilers

Tinkering

• Playground - testing profilers with small datasets