Optimised use of Oxford nanopore flowcells for hybrid assemblies

Optimised use of Oxford nanopore flowcells for hybrid assemblies

Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The...

Πλήρης περιγραφή

Λεπτομέρειες βιβλιογραφικής εγγραφής
Κύριοι συγγραφείς:	Lipworth, S, Pickford, H, Sanderson, N, Chau, KK, Kavanagh, J, Barker, L, Vaughan, A, Swann, J, Andersson, M, Jeffery, K, Morgan, M, Peto, TEA, Crook, DW, Stoesser, N, Walker, AS
Μορφή:	Journal article
Γλώσσα:	English
Έκδοση:	Microbiology Society 2020

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ανά: Constantinides, B, κ.ά.
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ανά: Lipworth, S, κ.ά.
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ανά: Davies, TJ, κ.ά.
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ανά: Lipworth, SIW, κ.ά.
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ανά: Matlock, W, κ.ά.
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ανά: Lewandowski, K, κ.ά.
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ανά: Stoesser, N, κ.ά.
Έκδοση: (2024)

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ανά: Lipworth, S, κ.ά.
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ανά: Street, TL, κ.ά.
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ανά: Matlock, W, κ.ά.
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ανά: Jabeen, MF, κ.ά.
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ανά: Kizny Gordon, A, κ.ά.
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ανά: Lipworth, S, κ.ά.
Έκδοση: (2022)

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ανά: Peto, L, κ.ά.
Έκδοση: (2021)

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ανά: Sanderson, N, κ.ά.
Έκδοση: (2018)

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ανά: Xu, Y, κ.ά.
Έκδοση: (2020)

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ανά: Samuel Lipworth, κ.ά.
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ανά: Maisha F. Jabeen, κ.ά.
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ανά: Yoon, CH, κ.ά.
Έκδοση: (2022)

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ανά: Shaw, LP, κ.ά.
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ανά: Xu, Y, κ.ά.
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ανά: Matlock, W, κ.ά.
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ανά: Eyre, DW, κ.ά.
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ανά: Samuel Lipworth, κ.ά.
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ανά: Eyre, DW, κ.ά.
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ανά: Hengyun Lu, κ.ά.
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ανά: Jiabao Cao, κ.ά.
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