MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations]
Background: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generat...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2017-05-01
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| Series: | F1000Research |
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| Online Access: | https://f1000research.com/articles/6-760/v1 |
| _version_ | 1818368933630050304 |
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| author | Miten Jain John R. Tyson Matthew Loose Camilla L.C. Ip David A. Eccles Justin O'Grady Sunir Malla Richard M. Leggett Ola Wallerman Hans J. Jansen Vadim Zalunin Ewan Birney Bonnie L. Brown Terrance P. Snutch Hugh E. Olsen MinION Analysis and Reference Consortium |
| author_facet | Miten Jain John R. Tyson Matthew Loose Camilla L.C. Ip David A. Eccles Justin O'Grady Sunir Malla Richard M. Leggett Ola Wallerman Hans J. Jansen Vadim Zalunin Ewan Birney Bonnie L. Brown Terrance P. Snutch Hugh E. Olsen MinION Analysis and Reference Consortium |
| author_sort | Miten Jain |
| collection | DOAJ |
| description | Background: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichia coli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry. Methods: We computed the error-rate estimates for insertions, deletions, and mismatches in MinION reads. Results: Run-time characteristics of the flow cell and run scripts for R9.0 were similar to those observed for R7.3 chemistry, but with an 8-fold increase in bases per second (from 30 bps in R7.3 and SQK-MAP005 library preparation, to 250 bps in R9.0) processed by individual nanopores, and less drop-off in yield over time. The 2-dimensional (“2D”) N50 read length was unchanged from the prior chemistry. Using the proportion of alignable reads as a measure of base-call accuracy, 99.9% of “pass” template reads from 1-dimensional (“1D”) experiments were mappable and ~97% from 2D experiments. The median identity of reads was ~89% for 1D and ~94% for 2D experiments. The total error rate (miscall + insertion + deletion ) decreased for 2D “pass” reads from 9.1% in R7.3 to 7.5% in R9.0 and for template “pass” reads from 26.7% in R7.3 to 14.5% in R9.0. Conclusions: These Phase 2 MinION experiments serve as a baseline by providing estimates for read quality, throughput, and mappability. The datasets further enable the development of bioinformatic tools tailored to the new R9.0 chemistry and the design of novel biological applications for this technology. Abbreviations: K: thousand, Kb: kilobase (one thousand base pairs), M: million, Mb: megabase (one million base pairs), Gb: gigabase (one billion base pairs). |
| first_indexed | 2024-12-13T23:15:49Z |
| format | Article |
| id | doaj.art-6065da08a0fa4c178dafec5b55813cd2 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-13T23:15:49Z |
| publishDate | 2017-05-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-6065da08a0fa4c178dafec5b55813cd22022-12-21T23:27:56ZengF1000 Research LtdF1000Research2046-14022017-05-01610.12688/f1000research.11354.112257MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations]Miten Jain0John R. Tyson1Matthew Loose2Camilla L.C. Ip3David A. Eccles4Justin O'Grady5Sunir Malla6Richard M. Leggett7Ola Wallerman8Hans J. Jansen9Vadim Zalunin10Ewan Birney11Bonnie L. Brown12Terrance P. Snutch13Hugh E. Olsen14MinION Analysis and Reference ConsortiumUniversity of California at Santa Cruz, Santa Cruz, CA, USAMichael Smith Laboratories and Djavad Mowfaghian Centre for Brain Health, University of British Columbia, Vancouver, CanadaSchool of Life Sciences, University of Nottingham, Nottingham, UKPeter Medawar Building for Pathogen Research, University of Oxford, Oxford, UKMalaghan Institute of Medical Research, Wellington, New ZealandNorwich Medical School, University of East Anglia, Norwich, UKSchool of Life Sciences, University of Nottingham, Nottingham, UKEarlham Institute, Norwich Research Park, Norwich, UKScience for Life Laboratory, IGP, Uppsala University, Uppsala, SwedenZF-screens B.V., Leiden, NetherlandsEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UKEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UKVirginia Commonwealth University, Richmond, VA, USAMichael Smith Laboratories and Djavad Mowfaghian Centre for Brain Health, University of British Columbia, Vancouver, CanadaUniversity of California at Santa Cruz, Santa Cruz, CA, USABackground: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichia coli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry. Methods: We computed the error-rate estimates for insertions, deletions, and mismatches in MinION reads. Results: Run-time characteristics of the flow cell and run scripts for R9.0 were similar to those observed for R7.3 chemistry, but with an 8-fold increase in bases per second (from 30 bps in R7.3 and SQK-MAP005 library preparation, to 250 bps in R9.0) processed by individual nanopores, and less drop-off in yield over time. The 2-dimensional (“2D”) N50 read length was unchanged from the prior chemistry. Using the proportion of alignable reads as a measure of base-call accuracy, 99.9% of “pass” template reads from 1-dimensional (“1D”) experiments were mappable and ~97% from 2D experiments. The median identity of reads was ~89% for 1D and ~94% for 2D experiments. The total error rate (miscall + insertion + deletion ) decreased for 2D “pass” reads from 9.1% in R7.3 to 7.5% in R9.0 and for template “pass” reads from 26.7% in R7.3 to 14.5% in R9.0. Conclusions: These Phase 2 MinION experiments serve as a baseline by providing estimates for read quality, throughput, and mappability. The datasets further enable the development of bioinformatic tools tailored to the new R9.0 chemistry and the design of novel biological applications for this technology. Abbreviations: K: thousand, Kb: kilobase (one thousand base pairs), M: million, Mb: megabase (one million base pairs), Gb: gigabase (one billion base pairs).https://f1000research.com/articles/6-760/v1Genomics |
| spellingShingle | Miten Jain John R. Tyson Matthew Loose Camilla L.C. Ip David A. Eccles Justin O'Grady Sunir Malla Richard M. Leggett Ola Wallerman Hans J. Jansen Vadim Zalunin Ewan Birney Bonnie L. Brown Terrance P. Snutch Hugh E. Olsen MinION Analysis and Reference Consortium MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] F1000Research Genomics |
| title | MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full | MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] |
| title_fullStr | MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] |
| title_short | MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: 1 approved, 2 approved with reservations] |
| title_sort | minion analysis and reference consortium phase 2 data release and analysis of r9 0 chemistry version 1 referees 1 approved 2 approved with reservations |
| topic | Genomics |
| url | https://f1000research.com/articles/6-760/v1 |
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