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Volumn 8, Issue 1, 2018, Pages

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

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NUCLEOTIDE;

EID: 85042230892     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-21484-w     Document Type: Article
Times cited : (51)

References (39)
  • 1
    • 84876936831 scopus 로고    scopus 로고
    • Effects of GC bias in next-generation-sequencing data on de novo genome assembly
    • Chen, Y. C., Liu, T., Yu, C. H., Chiang, T. Y. & Hwang, C. C. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One 8, e62856, https://doi.org/10.1371/journal.pone.0062856 (2013).
    • (2013) PloS One , vol.8 , pp. e62856
    • Chen, Y.C.1    Liu, T.2    Yu, C.H.3    Chiang, T.Y.4    Hwang, C.C.5
  • 2
    • 84861548193 scopus 로고    scopus 로고
    • Summarizing and correcting the GC content bias in high-throughput sequencing
    • Benjamini, Y. & Speed, T. P. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40, e72, https://doi.org/10.1093/nar/gks001 (2012).
    • (2012) Nucleic Acids Res , vol.40 , pp. e72
    • Benjamini, Y.1    Speed, T.P.2
  • 3
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138, https://doi.org/10.1126/science.1162986 (2009).
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1
  • 4
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule, real-time sequencing
    • Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7, 461-465, https://doi.org/10.1038/nmeth.1459 (2010).
    • (2010) Nat Methods , vol.7 , pp. 461-465
    • Flusberg, B.A.1
  • 5
    • 84926472171 scopus 로고    scopus 로고
    • Improved data analysis for the MinION nanopore sequencer
    • Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat Methods 12, 351-356, https://doi.org/10.1038/nmeth.3290 (2015).
    • (2015) Nat Methods , vol.12 , pp. 351-356
    • Jain, M.1
  • 6
    • 84998996876 scopus 로고    scopus 로고
    • The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community
    • Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17, 239, https://doi.org/10.1186/s13059-016-1103-0 (2016).
    • (2016) Genome Biol , vol.17 , pp. 239
    • Jain, M.1    Olsen, H.E.2    Paten, B.3    Akeson, M.4
  • 7
    • 77957051540 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Korlach, J. et al. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 472, 431-455, https://doi.org/10.1016/S0076-6879(10)72001-2 (2010).
    • (2010) Methods Enzymol , vol.472 , pp. 431-455
    • Korlach, J.1
  • 8
    • 84980361397 scopus 로고    scopus 로고
    • Real-time selective sequencing using nanopore technology
    • Loose, M., Malla, S. & Stout, M. Real-time selective sequencing using nanopore technology. Nat Methods 13, 751-754, https://doi.org/10.1038/nmeth.3930 (2016).
    • (2016) Nat Methods , vol.13 , pp. 751-754
    • Loose, M.1    Malla, S.2    Stout, M.3
  • 9
    • 84934284959 scopus 로고    scopus 로고
    • Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
    • Quick, J. et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 16, 114, https://doi.org/10.1186/s13059-015-0677-2 (2015).
    • (2015) Genome Biol , vol.16 , pp. 114
    • Quick, J.1
  • 10
    • 84947299022 scopus 로고    scopus 로고
    • PacBio sequencing and its applications
    • Rhoads, A. & Au, K. F. PacBio Sequencing and Its Applications. Genomics Proteomics Bioinformatics 13, 278-289, https://doi.org/10.1016/j.gpb.2015.08.002 (2015).
    • (2015) Genomics Proteomics Bioinformatics , vol.13 , pp. 278-289
    • Rhoads, A.1    Au, K.F.2
  • 11
    • 84930851165 scopus 로고    scopus 로고
    • Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
    • Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33, 623-630, https://doi.org/10.1038/nbt.3238 (2015).
    • (2015) Nat Biotechnol , vol.33 , pp. 623-630
    • Berlin, K.1
  • 12
    • 84929697731 scopus 로고    scopus 로고
    • Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events
    • Tilgner, H. et al. Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. Nat Biotechnol 33, 736-742, https://doi.org/10.1038/nbt.3242 (2015).
    • (2015) Nat Biotechnol , vol.33 , pp. 736-742
    • Tilgner, H.1
  • 13
    • 85019741923 scopus 로고    scopus 로고
    • Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
    • Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 12, 1261-1276, https://doi.org/10.1038/nprot.2017.066 (2017).
    • (2017) Nat Protoc , vol.12 , pp. 1261-1276
    • Quick, J.1
  • 14
    • 84958068536 scopus 로고    scopus 로고
    • Real-time, portable genome sequencing for Ebola surveillance
    • Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228-232, https://doi.org/10.1038/nature16996 (2016).
    • (2016) Nature , vol.530 , pp. 228-232
    • Quick, J.1
  • 15
    • 85018305549 scopus 로고    scopus 로고
    • Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples
    • Votintseva, A. A. et al. Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples. J Clin Microbiol 55, 1285-1298, https://doi.org/10.1128/JCM.02483-16 (2017).
    • (2017) J Clin Microbiol , vol.55 , pp. 1285-1298
    • Votintseva, A.A.1
  • 16
    • 84942518081 scopus 로고    scopus 로고
    • Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    • Greninger, A. L. et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7, 99, https://doi.org/10.1186/s13073-015-0220-9 (2015).
    • (2015) Genome Med , vol.7 , pp. 99
    • Greninger, A.L.1
  • 17
    • 85010763983 scopus 로고    scopus 로고
    • Highly parallel direct RNA sequencing on an array of nanopores
    • Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. bioRxiv, https://doi.org/10.1101/068809 (2017).
    • (2017) BioRxiv
    • Garalde, D.R.1
  • 18
    • 85013157844 scopus 로고    scopus 로고
    • Mapping DNA methylation with high-throughput nanopore sequencing
    • Rand, A. C. et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods 14, 411-413, https://doi.org/10.1038/nmeth.4189 (2017).
    • (2017) Nat Methods , vol.14 , pp. 411-413
    • Rand, A.C.1
  • 19
    • 85029555861 scopus 로고    scopus 로고
    • Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
    • Smith, A. M., Jain, M., Mulroney, L.. Garalde, D. R. & Akeson, M. Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing. bioRxiv, https://doi.org/10.1101/132274 (2017).
    • (2017) BioRxiv
    • Smith, A.M.1    Jain, M.2    Mulroney, L.3    Garalde, D.R.4    Akeson, M.5
  • 20
    • 84925352769 scopus 로고    scopus 로고
    • Assessing the performance of the Oxford Nanopore Technologies MinION
    • Laver, T. et al. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif 3, 1-8, https://doi.org/10.1016/j.bdq.2015.02.001 (2015).
    • (2015) Biomol Detect Quantif , vol.3 , pp. 1-8
    • Laver, T.1
  • 21
    • 84983605356 scopus 로고    scopus 로고
    • Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
    • Oikonomopoulos, S., Wang, Y. C., Djambazian, H., Badescu, D. & Ragoussis, J. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6, 31602, https://doi.org/10.1038/srep31602 (2016).
    • (2016) Sci Rep , vol.6 , pp. 31602
    • Oikonomopoulos, S.1    Wang, Y.C.2    Djambazian, H.3    Badescu, D.4    Ragoussis, J.5
  • 22
    • 84946557268 scopus 로고    scopus 로고
    • Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    • Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25, 1750-1756, https://doi.org/10.1101/gr.191395.115 (2015).
    • (2015) Genome Res , vol.25 , pp. 1750-1756
    • Goodwin, S.1
  • 23
    • 84938851187 scopus 로고    scopus 로고
    • MinION nanopore sequencing of an influenza genome
    • Wang, J., Moore, N. E., Deng, Y. M., Eccles, D. A. & Hall, R. J. MinION nanopore sequencing of an influenza genome. Front Microbiol 6, 766, https://doi.org/10.3389/fmicb.2015.00766 (2015).
    • (2015) Front Microbiol , vol.6 , pp. 766
    • Wang, J.1    Moore, N.E.2    Deng, Y.M.3    Eccles, D.A.4    Hall, R.J.5
  • 24
    • 85019264879 scopus 로고    scopus 로고
    • Genome assembly using Nanopore-guided long and error-free DNA reads
    • Madoui, M. A. et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 16, 327, https://doi.org/10.1186/s12864-015-1519-z (2015).
    • (2015) BMC Genomics , vol.16 , pp. 327
    • Madoui, M.A.1
  • 25
    • 84936764311 scopus 로고    scopus 로고
    • Scaffolding of a bacterial genome using MinION nanopore sequencing
    • Karlsson, E., Larkeryd, A., Sjodin, A., Forsman, M. & Stenberg, P. Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci Rep 5, 11996, https://doi.org/10.1038/srep11996 (2015).
    • (2015) Sci Rep , vol.5 , pp. 11996
    • Karlsson, E.1    Larkeryd, A.2    Sjodin, A.3    Forsman, M.4    Stenberg, P.5
  • 26
    • 84878234942 scopus 로고    scopus 로고
    • Characterizing and measuring bias in sequence data
    • Ross, M. G. et al. Characterizing and measuring bias in sequence data. Genome Biol 14, R51, https://doi.org/10.1186/gb-2013-14-5-r51 (2013).
    • (2013) Genome Biol , vol.14 , pp. R51
    • Ross, M.G.1
  • 27
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12, R18, https://doi.org/10.1186/gb-2011-12-2-r18 (2011).
    • (2011) Genome Biol , vol.12 , pp. R18
    • Aird, D.1
  • 31
    • 85020235714 scopus 로고    scopus 로고
    • Nanopore sequencing and assembly of a human genome with ultra-long reads
    • Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. bioRxiv, https://doi.org/10.1101/128835 (2017).
    • (2017) BioRxiv
    • Jain, M.1
  • 32
    • 85033690821 scopus 로고    scopus 로고
    • De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    • Schmidt, M. H. et al. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. Plant Cell 29, 2336-2348, https://doi.org/10.1105/tpc.17.00521 (2017).
    • (2017) Plant Cell , vol.29 , pp. 2336-2348
    • Schmidt, M.H.1
  • 33
    • 85034431348 scopus 로고    scopus 로고
    • Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D
    • Salazar, A. N. et al. Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D. FEMS Yeast Res 17, https://doi.org/10.1093/femsyr/fox074 (2017).
    • (2017) FEMS Yeast Res , vol.17
    • Salazar, A.N.1
  • 34
    • 85026912929 scopus 로고    scopus 로고
    • Rapid de novo assembly of the European eel genome from nanopore sequencing reads
    • Jansen, H. J. et al. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Sci Rep 7, 7213, https://doi.org/10.1038/s41598-017-07650-6 (2017).
    • (2017) Sci Rep , vol.7 , pp. 7213
    • Jansen, H.J.1
  • 35
    • 85030624392 scopus 로고    scopus 로고
    • High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing
    • Fournier, T. et al. High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. G3 (Bethesda) 7, 3243-3250, https://doi.org/10.1534/g3.117.300128 (2017).
    • (2017) G3 (Bethesda) , vol.7 , pp. 3243-3250
    • Fournier, T.1
  • 36
    • 84970974695 scopus 로고    scopus 로고
    • Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION
    • Urban, J. M., Bliss, J., Lawrence, C. E. & Gerbi, S. A. Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. bioRxiv, https://doi.org/10.1101/019281 (2015).
    • (2015) BioRxiv
    • Urban, J.M.1    Bliss, J.2    Lawrence, C.E.3    Gerbi, S.A.4
  • 37
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595, https://doi.org/10.1093/bioinformatics/btp698 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842, https://doi.org/10.1093/bioinformatics/btq033 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 39
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079, https://doi.org/10.1093/bioinformatics/btp352 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1


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