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.

Scholz, M.; Ward, D.V.; Pasolli, E.; Tolio, T.; Zolfo, M.; Asnicar, F.; Truong, D.T.; Tett, A.; Morrow, A.L.; Segata, N. (2016). Strain-level microbial epidemiology and population genomics from shotgun metagenomics. NATURE METHODS, 13 (5): 435-8-438. doi: 10.1038/nmeth.3802 handle: http://hdl.handle.net/10449/67610

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Scholz, Matthias
Primo
;
2016

Abstract

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.
Metagenomics
Strain-level metagenomics
Pangenome
Sequence analysis methods
Genomics
Settore BIO/19 - MICROBIOLOGIA GENERALE
Scholz, M.; Ward, D.V.; Pasolli, E.; Tolio, T.; Zolfo, M.; Asnicar, F.; Truong, D.T.; Tett, A.; Morrow, A.L.; Segata, N. (2016). Strain-level microbial epidemiology and population genomics from shotgun metagenomics. NATURE METHODS, 13 (5): 435-8-438. doi: 10.1038/nmeth.3802 handle: http://hdl.handle.net/10449/67610
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/67610
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