MinION Analysis and Reference Consortium: Phase 1 data release and analysis

Camilla L. C. Ip; Matthew  Loose; John R. Tyson; Mariateresa de Cesare; Bonnie L. Brown; Miten Jain; Richard M. Leggett; David A. Eccles; Vadim Zalunin; John M. Urban; Paolo Piazza; Rory J. Bowden; Benedict Paten; Solomon Mwaigwisya; Elizabeth M. Batty; Jared T. Simpson; Terrance P. Snutch; Ewan Birney; David Buck; Sara Goodwin; Hans J. Jansen; Justin O'Grady; Hugh E. Olsen

doi:10.12688/f1000research.7201.1

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

Camilla L. C. Ip, Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, Vadim Zalunin, John M. Urban, Paolo Piazza, Rory J. Bowden, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney, David Buck, Sara GoodwinHans J. Jansen, Justin O'Grady, Hugh E. Olsen

Norwich Medical School

Research output: Contribution to journal › Article › peer-review

199 Citations (Scopus)

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Abstract

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.

Original language	English
Article number	1075
Journal	F1000Research
Volume	4
Issue number	1075
DOIs	https://doi.org/10.12688/f1000research.7201.1
Publication status	Published - 15 Oct 2015

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Cite this

Ip, C. L. C., Loose, M., Tyson, J. R., de Cesare, M., Brown, B. L., Jain, M., Leggett, R. M., Eccles, D. A., Zalunin, V., Urban, J. M., Piazza, P., Bowden, R. J., Paten, B., Mwaigwisya, S., Batty, E. M., Simpson, J. T., Snutch, T. P., Birney, E., Buck, D., ... Olsen, H. E. (2015). MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research, 4(1075), [1075]. https://doi.org/10.12688/f1000research.7201.1

Ip, Camilla L. C. ; Loose, Matthew ; Tyson, John R. ; de Cesare, Mariateresa ; Brown, Bonnie L. ; Jain, Miten ; Leggett, Richard M. ; Eccles, David A. ; Zalunin, Vadim ; Urban, John M. ; Piazza, Paolo ; Bowden, Rory J. ; Paten, Benedict ; Mwaigwisya, Solomon ; Batty, Elizabeth M. ; Simpson, Jared T. ; Snutch, Terrance P. ; Birney, Ewan ; Buck, David ; Goodwin, Sara ; Jansen, Hans J. ; O'Grady, Justin ; Olsen, Hugh E. / MinION Analysis and Reference Consortium: Phase 1 data release and analysis. In: F1000Research. 2015 ; Vol. 4, No. 1075.

@article{6043a84a95eb4bca872cb2bbeeee538b,

title = "MinION Analysis and Reference Consortium: Phase 1 data release and analysis",

abstract = "The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION{\texttrademark} Access Programme (MAP) was initiated by Oxford Nanopore Technologies{\texttrademark} in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance. ",

author = "Ip, {Camilla L. C.} and Matthew Loose and Tyson, {John R.} and {de Cesare}, Mariateresa and Brown, {Bonnie L.} and Miten Jain and Leggett, {Richard M.} and Eccles, {David A.} and Vadim Zalunin and Urban, {John M.} and Paolo Piazza and Bowden, {Rory J.} and Benedict Paten and Solomon Mwaigwisya and Batty, {Elizabeth M.} and Simpson, {Jared T.} and Snutch, {Terrance P.} and Ewan Birney and David Buck and Sara Goodwin and Jansen, {Hans J.} and Justin O'Grady and Olsen, {Hugh E.}",

note = "Date of Acceptance: 23/11/2015 {\textcopyright} 2015 Ip CLC et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.",

year = "2015",

month = oct,

day = "15",

doi = "10.12688/f1000research.7201.1",

language = "English",

volume = "4",

journal = "F1000Research",

issn = "2046-1402",

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Ip, CLC, Loose, M, Tyson, JR, de Cesare, M, Brown, BL, Jain, M, Leggett, RM, Eccles, DA, Zalunin, V, Urban, JM, Piazza, P, Bowden, RJ, Paten, B, Mwaigwisya, S, Batty, EM, Simpson, JT, Snutch, TP, Birney, E, Buck, D, Goodwin, S, Jansen, HJ, O'Grady, J & Olsen, HE 2015, 'MinION Analysis and Reference Consortium: Phase 1 data release and analysis', F1000Research, vol. 4, no. 1075, 1075. https://doi.org/10.12688/f1000research.7201.1

MinION Analysis and Reference Consortium: Phase 1 data release and analysis. / Ip, Camilla L. C.; Loose, Matthew ; Tyson, John R.; de Cesare, Mariateresa; Brown, Bonnie L.; Jain, Miten; Leggett, Richard M.; Eccles, David A.; Zalunin, Vadim; Urban, John M.; Piazza, Paolo; Bowden, Rory J.; Paten, Benedict; Mwaigwisya, Solomon; Batty, Elizabeth M.; Simpson, Jared T.; Snutch, Terrance P.; Birney, Ewan; Buck, David; Goodwin, Sara; Jansen, Hans J.; O'Grady, Justin; Olsen, Hugh E.

In: F1000Research, Vol. 4, No. 1075, 1075, 15.10.2015.

Research output: Contribution to journal › Article › peer-review

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T1 - MinION Analysis and Reference Consortium: Phase 1 data release and analysis

AU - Ip, Camilla L. C.

AU - Loose, Matthew

AU - Tyson, John R.

AU - de Cesare, Mariateresa

AU - Brown, Bonnie L.

AU - Jain, Miten

AU - Leggett, Richard M.

AU - Eccles, David A.

AU - Zalunin, Vadim

AU - Urban, John M.

AU - Piazza, Paolo

AU - Bowden, Rory J.

AU - Paten, Benedict

AU - Mwaigwisya, Solomon

AU - Batty, Elizabeth M.

AU - Simpson, Jared T.

AU - Snutch, Terrance P.

AU - Birney, Ewan

AU - Buck, David

AU - Goodwin, Sara

AU - Jansen, Hans J.

AU - O'Grady, Justin

AU - Olsen, Hugh E.

N1 - Date of Acceptance: 23/11/2015 © 2015 Ip CLC et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PY - 2015/10/15

Y1 - 2015/10/15

N2 - The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.

AB - The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.

U2 - 10.12688/f1000research.7201.1

DO - 10.12688/f1000research.7201.1

M3 - Article

VL - 4

JO - F1000Research

JF - F1000Research

SN - 2046-1402

IS - 1075

M1 - 1075

ER -