domains / families / science / metaphlan-profiling

metaphlan-profiling

separate

Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads). Covers why a MetaPhlAn percentage is a cell fraction (genome-size-normalized taxonomic abundance) and must never be merged with Kraken/Bracken read fractions, kSGB vs uSGB units for quantifying database-absent taxa, the unknown-fraction rescaling and its version-default flip, --index pinning as a batch variable, and when mOTUs3 or sourmash gather beat marker profiling. Use when profiling who-is-there with high precision, needing HMP-comparable species abundances, quantifying novel taxa, or deciding marker-gene vs k-mer profiling. For k-mer classification see kraken-classification; for strains see strain-tracking; for 16S amplicon see the microbiome category.

When to use

• Profiling who-is-there with high precision
• Needing HMP-comparable species abundances
• Quantifying novel taxa
• Deciding marker-gene vs k-mer profiling
• Marker-gene species/SGB profiling
• Detecting clade-specific marker genes
• Normalizing to genome-size-aware relative abundance

When not to use

• K-mer read classification
• Strain-resolved SNV haplotypes
• Functional profiling
• Compositional stats and plotting
• 16S amplicon analysis
• Merging MetaPhlAn percentages with Kraken/Bracken percentages

Skill page

Source