Assessing taxonomic metagenome profilers with OPAL
Open accessPublished version of a preprint
Abstract
The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. OPAL is freely available at https://github.com/CAMI-challenge/OPAL .
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
MetaPhlAn 2.7, mOTUs 2.51, and Bracken 2.5 have consistently been shown to outperform other methods across multiple evaluations.
“These three profiling tools have consistently been shown to outperform other methods across multiple evaluations (McIntyre et al., 2017; Meyer et al., 2019; Milanese et al., 2019; Sczyrba et al., 2017; Truong et al., 2015; Ye et al., 2019).”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Meyer et al., 2019
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 40 · Cited by 80
- Authors
- Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A. C., & Koslicki, D.
- Affiliations
- Helmholtz Centre for Infection Research (DE)
- German Center for Infection Research (DE)
- Bielefeld University (DE)
- University of California San Diego (US)
- Oregon State University (US)
- Corresponding author
- McHardy, Alice C.
- Koslicki, David
- Venue
- Genome Biology
- Published
- 2019-03-04
- Volume
- 20
- Issue
- 1
- Pages
- 51-51
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC6398228
- OpenAlex
- W2951676949
- Cited by
- 80
- References
- 40
- Citations by year
- 2026: 4 · 2025: 11 · 2024: 12 · 2023: 11 · 2022: 15 · 2021: 14 · 2020: 8 · 2019: 4
- FWCI
- 3.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- HZI (Helmholtz Centre for Infection Research) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (1664803)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- opal, CAMI challenge, performance indicators, benchmarking, Human Microbiome Project, microbial community composition
- MeSH terms
- Classification, Humans, Software, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
