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.

Strain-level microbial epidemiology and population genomics from shotgun metagenomics / Scholz, Matthias Uwe; Ward, Doyle V.; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian James; Morrow, Ardythe L.; Segata, Nicola. - In: NATURE METHODS. - ISSN 1548-7091. - 13:5(2016), pp. 435-438. [10.1038/nmeth.3802]

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Scholz, Matthias Uwe;Pasolli, Edoardo;Zolfo, Moreno;Asnicar, Francesco;Truong, Duy Tin;Tett, Adrian James;Segata, Nicola
2016-01-01

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.
2016
5
Scholz, Matthias Uwe; Ward, Doyle V.; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian James; Morrow,...espandi
Strain-level microbial epidemiology and population genomics from shotgun metagenomics / Scholz, Matthias Uwe; Ward, Doyle V.; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian James; Morrow, Ardythe L.; Segata, Nicola. - In: NATURE METHODS. - ISSN 1548-7091. - 13:5(2016), pp. 435-438. [10.1038/nmeth.3802]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/147879
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