| name | metaphlan |
| description | Marker-gene taxonomic profiling of metagenomes. Use this skill when working with metaphlan: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/biobakery/MetaPhlAn. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["taxonomy","marker","profiling"] |
| upstream | https://github.com/biobakery/MetaPhlAn |
MetaPhlAn
Upstream: biobakery/MetaPhlAn
Citation
Blanco-Míguez, A. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat. Biotechnol. 41, 1633–1644 (2023). https://doi.org/10.1038/s41587-023-01688-w
See also docs/references.md.
Analytical thinking
MetaPhlAn 4 profiles via SGB-specific marker genes (species-level genome
bins), including many unknown SGBs built from MAGs — not only named species.
Detection uses a sufficient fraction of markers (default 20%); abundance uses
within-sample-normalized average marker coverage.
From the paper / practical implications:
- Expands profiling into uncharacterized diversity vs isolate-only markers.
- Presence calls aim for low false positives; coverage ~≥0.5× was associated with
reliable detection in isolate-based checks in that work — rare taxa near noise
need cautious language.
- MetaPhlAn authors note high false-positive rates for some Bracken settings in
their comparisons — do not treat Kraken+Bracken and MetaPhlAn as
interchangeable species tables.
- Cannot report taxa lacking markers in the installed database.
Often invoked inside HUMAnN; use this skill when MetaPhlAn outputs/parameters
are primary deliverables.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Input | Dehosted PE/SE FASTQ | From kneaddata |
| Database | MetaPhlAn DB matching software version | Pinned release (SGB DB) |
| RAM | 16–32 GB | 64 GB |
How to run
metaphlan \
temp/hr/${id}_1.fastq,temp/hr/${id}_2.fastq \
--input_type fastq \
--bowtie2out temp/metaphlan/${id}.bowtie2.bz2 \
-o result/metaphlan/${id}_profile.txt \
--nproc 8
Merge profiles across samples with MetaPhlAn utility scripts / HUMAnN join tools.
Interpretation
| Output | Means | Does not mean |
|---|
| Relative abundance | Marker-supported composition | Absolute CFU/load |
| SGB / unknown clade | Marker package present | Cultured species name |
| Unclassified | No markers hit | Community is empty |
Decision tree
Need marker-based species/SGBs?
├─ Yes → metaphlan (alone or via humann)
├─ Pathways too → humann
├─ Joint DNA+AA read class → metabuli
├─ Custom large DNA DB → kraken2 (+ bracken)
└─ Sketch containment → sylph
Related skills
humann · kraken2 · motus · metabuli · sylph · visualization · tool-selection
