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metagenomics-pipeline

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End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

When to use

• profiling shotgun metagenomic samples end to end
• chaining classification, abundance, and function
• orchestrating controls and host depletion
• Kraken2/Bracken taxonomic classification
• MetaPhlAn profiling
• HUMAnN3 functional analysis

When not to use

• resistome
• strains
• assembly

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