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™ 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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Camilla L C
authors.initials: CLC
authors.lastname: Ip
authors.affiliation: School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Loose
authors.affiliation: Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.
authors.forename: John R
authors.initials: JR
authors.lastname: Tyson
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Mariateresa
authors.initials: M
authors.lastname: de Cesare
authors.affiliation: Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Bonnie L
authors.initials: BL
authors.lastname: Brown
authors.affiliation: University of California, Santa Cruz, Santa Cruz, CA, USA.
authors.forename: Miten
authors.initials: M
authors.lastname: Jain
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, UK.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Leggett
authors.affiliation: Malaghan Institute of Medical Research, Wellington, New Zealand.
authors.forename: David A
authors.initials: DA
authors.lastname: Eccles
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Vadim
authors.initials: V
authors.lastname: Zalunin
authors.affiliation: Division of Biology and Medicine, Brown University, Providence, RI, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Urban
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Paolo
authors.initials: P
authors.lastname: Piazza
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Rory J
authors.initials: RJ
authors.lastname: Bowden
authors.affiliation: University of California, Santa Cruz, Santa Cruz, CA, USA.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich, UK.
authors.forename: Solomon
authors.initials: S
authors.lastname: Mwaigwisya
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Batty
authors.affiliation: Informatics and Biocomputing, Ontario Institute for Cancer Research, ON, Canada.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
authors.affiliation: Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.
authors.forename: Terrance P
authors.initials: TP
authors.lastname: Snutch
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: David
authors.initials: D
authors.lastname: Buck
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Goodwin
authors.affiliation: ZF-screens B.V., Leiden, Netherlands.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Jansen
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich, UK.
authors.forename: Justin
authors.initials: J
authors.lastname: O'Grady
authors.affiliation: University of California, Santa Cruz, Santa Cruz, CA, USA.
authors.forename: Hugh E
authors.initials: HE
authors.lastname: Olsen
keywords: MinION; NanoOK; data release; long reads; marginAlign; minoTour; nanopore sequencing; third-generation sequencing
references.citation: Gigascience. 2014 Oct 20;3:22
references.pmid: 25386338
references.citation: Brief Bioinform. 2016 Jan;17(1):154-79
references.pmid: 26026159
references.citation: Biophys J. 2012 May 16;102(10):L37-9
references.pmid: 22677395
references.citation: Biophys J. 1999 Dec;77(6):3227-33
references.pmid: 10585944
references.citation: Genome Res. 2011 Mar;21(3):487-93
references.pmid: 21209072
references.citation: Front Microbiol. 2015 Aug 18;6:766
references.pmid: 26347715
references.citation: Bioinformatics. 2015 Jan 1;31(1):114-5
references.pmid: 25173419
references.citation: Genome Med. 2015 Sep 29;7:99
references.pmid: 26416663
references.citation: Nano Lett. 2011 Jun 8;11(6):2247-50
references.pmid: 21604710
references.citation: Nat Biotechnol. 2015 Oct;33(10):1087-91
references.pmid: 26352647
references.citation: Gigascience. 2015 Mar 26;4:12
references.pmid: 25815165
references.citation: Sci Rep. 2015 Jul 07;5:11996
references.pmid: 26149338
references.citation: BMC Biol. 2014 Nov 12;12:87
references.pmid: 25387460
references.citation: Nat Biotechnol. 2014 Aug;32(8):829-33
references.pmid: 24964173
references.citation: Bioinformatics. 2007 Jan 15;23(2):e24-9
references.pmid: 17237099
references.citation: Biomol Detect Quantif. 2015 Mar;3:1-8
references.pmid: 26753127
references.citation: J Am Chem Soc. 2010 Dec 22;132(50):17961-72
references.pmid: 21121604
references.citation: Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3
references.pmid: 8943010
references.citation: Nat Methods. 2015 Apr;12(4):351-6
references.pmid: 25686389
references.citation: Genome Res. 2015 Nov;25(11):1750-6
references.pmid: 26447147
references.citation: PLoS One. 2011;6(10):e25723
references.pmid: 21991340
references.citation: PeerJ. 2015 Nov 24;3:e1441
references.pmid: 26623194
references.citation: Genome Biol. 2014 Mar 03;15(3):R46
references.pmid: 24580807
references.citation: Nat Biotechnol. 2012 Apr 10;30(4):295-6
references.pmid: 22491260
references.citation: Bioinformatics. 2014 Dec 1;30(23):3399-401
references.pmid: 25143291
references.citation: Chem Commun (Camb). 2010 Nov 21;46(43):8195-7
references.pmid: 20927439
references.citation: Curr Opin Chem Biol. 2006 Dec;10(6):628-37
references.pmid: 17113816
references.citation: Bioinformatics. 2016 Jan 1;32(1):142-4
references.pmid: 26382197
references.citation: Nat Methods. 2015 Aug;12(8):733-5
references.pmid: 26076426
references.citation: F1000Res. 2015 Jan 21;4:17
references.pmid: 25901276
references.citation: Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16060-5
references.pmid: 20798343
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Nat Biotechnol. 2012 Feb 14;30(4):344-8
references.pmid: 22334048
references.citation: Nat Biotechnol. 2015 Mar;33(3):296-300
references.pmid: 25485618