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| Auteurs principaux: | , , , , , |
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| Format: | Artículo científico |
| Langue: | en |
| Publié: |
Nucleic acids research
2025
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| Sujets: | |
| Accès en ligne: | https://pubmed.ncbi.nlm.nih.gov/40331433/ |
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| _version_ | 1868266206577819649 |
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| author | Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C |
| author_facet | Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C |
| collection | PubMed - marine biology |
| contents | CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software. Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C Software Metagenomics Benchmarking Metagenome Internet Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/. |
| format | Artículo científico |
| id | pubmed_40331433 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Nucleic acids research |
| record_format | pubmed |
| spellingShingle | CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software. Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C Software Metagenomics Benchmarking Metagenome Internet CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software. Meyer, Fernando Robertson, Gary Deng, Zhi-Luo Koslicki, David Gurevich, Alexey McHardy, Alice C Software Metagenomics Benchmarking Metagenome Internet Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/. |
| title | CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software. |
| topic | Software Metagenomics Benchmarking Metagenome Internet |
| url | https://pubmed.ncbi.nlm.nih.gov/40331433/ |