ArticleGenome biology2019
Assessing taxonomic metagenome profilers with OPAL.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.Microbiome · 2025Article
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software.Nucleic acids research · 2025Article
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- Memory-boundGenome research · 2024Article
- MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies.Nature communications · 2024Article
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.Bioinformatics (Oxford, England) · 2024Article
- ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.Bioinformatics (Oxford, England) · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.Bioinformatics (Oxford, England) · 2024Article
- Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.Scientific data · 2024Article
- CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.Frontiers in microbiology · 2024Article
- Challenges and opportunities in sharing microbiome data and analyses.Nature microbiology · 2023Review
- Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.Nature biotechnology · 2023Article
- Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.Microorganisms · 2023Article
- Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.Microbiome · 2023Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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 .
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