Publication date: Oct 08, 2024
Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph’s ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph took
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| Concepts | Keywords |
|---|---|
| Accurate | Ani |
| Biotechnol | Based |
| Genomes | Containment |
| Parkinson | Detection |
| Estimates | |
| Estimation | |
| Fold | |
| Level | |
| Metagenome | |
| Metagenomes | |
| Pd | |
| Profiling | |
| Rapid | |
| Species | |
| Sylph |
Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | Parkinson disease |
| pathway | KEGG | Parkinson disease |
| drug | DRUGBANK | Butyric Acid |