Journal
NATURE METHODS
Volume 13, Issue 5, Pages 435-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/NMETH.3802
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Funding
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272200900018C]
- European Union under REA grant [PCIG13-GA-2013-618833]
- Centre for Integrative Biology, University of Trento
- MIUR Futuro in Ricerca [RBFR13EWWI_001]
- Fondazione Caritro
- 'Terme di Comano'
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Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.
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