ArticleNature biotechnology2025
Rapid species-level metagenome profiling and containment estimation with sylph.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.Cell reports · 2026Article
- Divergent microbial functional pathways and declining redundancy in lake sediments across eutrophication gradients.Nature communications · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Article
- TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.Nature genetics · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.Comprehensive Physiology · 2026Article
- ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.bioRxiv : the preprint server for biology · 2026Article
- A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease.bioRxiv : the preprint server for biology · 2026Article
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.Nature communications · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- Evolution of pandemic cholera at its global source.Nature · 2026Article
10 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
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 <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.
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