Fast and flexible bacterial genomic epidemiology with PopPUNK.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
02 2019
02 2019
Historique:
received:
05
07
2018
accepted:
10
12
2018
pubmed:
27
1
2019
medline:
30
5
2019
entrez:
26
1
2019
Statut:
ppublish
Résumé
The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (
Identifiants
pubmed: 30679308
pii: gr.241455.118
doi: 10.1101/gr.241455.118
pmc: PMC6360808
doi:
Banques de données
figshare
['10.6084/m9.figshare.6683624']
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
304-316Subventions
Organisme : Wellcome Trust
ID : 104169/Z/14/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R003076/1
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R37 AI038446
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI038446
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI105168
Pays : United States
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 098051
Pays : United Kingdom
Informations de copyright
© 2019 Lees et al.; Published by Cold Spring Harbor Laboratory Press.
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