Assessing taxonomic metagenome profilers with OPAL.
Bioboxes
Metagenomics
Performance metrics
Taxonomic profiling
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
04 03 2019
04 03 2019
Historique:
received:
08
08
2018
accepted:
31
01
2019
entrez:
6
3
2019
pubmed:
6
3
2019
medline:
22
3
2019
Statut:
epublish
Résumé
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 .
Identifiants
pubmed: 30832730
doi: 10.1186/s13059-019-1646-y
pii: 10.1186/s13059-019-1646-y
pmc: PMC6398228
doi:
Types de publication
Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
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