메뉴 건너뛰기




Volumn 6, Issue , 2016, Pages

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

Author keywords

[No Author keywords available]

Indexed keywords

AGROBACTERIUM TUMEFACIENS; GENETIC DATABASE; GENETICS;

EID: 84976585777     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep28625     Document Type: Article
Times cited : (24)

References (41)
  • 1
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • Mardis, E. R. A decade's perspective on DNA sequencing technology. Nature 470, 198-203 (2011).
    • (2011) Nature , vol.470 , pp. 198-203
    • Mardis, E.R.1
  • 2
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145 (2008).
    • (2008) Nat. Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 3
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1
  • 4
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 5
    • 77952425335 scopus 로고    scopus 로고
    • Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
    • Deschamps, S. & Campbell, M. A. Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Mol. Breed. 25, 553-570 (2010).
    • (2010) Mol. Breed , vol.25 , pp. 553-570
    • Deschamps, S.1    Campbell, M.A.2
  • 6
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379 (2011).
    • (2011) PLoS One , vol.6 , pp. e19379
    • Elshire, R.J.1
  • 7
    • 84988945264 scopus 로고    scopus 로고
    • Chromatin accessibility: A window into the genome
    • Tsompana, M. & Buck, M. J. Chromatin accessibility: A window into the genome. Epigenetics Chromatin 7, 33 (2014).
    • (2014) Epigenetics Chromatin , vol.7 , pp. 33
    • Tsompana, M.1    Buck, M.J.2
  • 8
    • 84856498057 scopus 로고    scopus 로고
    • DNA methylome analysis using short bisulfite sequencing data
    • Krueger, F., Kreck, B., Franke, A. & Andrews, S. R. DNA methylome analysis using short bisulfite sequencing data. Nat. Methods 9, 145-151 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 145-151
    • Krueger, F.1    Kreck, B.2    Franke, A.3    Andrews, S.R.4
  • 9
    • 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 (2009).
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1
  • 10
    • 84959097553 scopus 로고    scopus 로고
    • No assembly required: Full-length MHC class i allele discovery by PacBio circular consensus sequencing
    • Westbrook, C. J. et al. No assembly required: full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum. Immunol. 76, 891-896 (2015).
    • (2015) Hum. Immunol , vol.76 , pp. 891-896
    • Westbrook, C.J.1
  • 11
    • 84988565996 scopus 로고    scopus 로고
    • Improved OUT-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering
    • Franzén, O. et al. Improved OUT-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. Microbiome 3, 43 (2015).
    • (2015) Microbiome , vol.3 , pp. 43
    • Franzén, O.1
  • 12
    • 84938423867 scopus 로고    scopus 로고
    • Assembly and diploid architecture of an individual human genome via single-molecule technologies
    • Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780-786 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 780-786
    • Pendleton, M.1
  • 13
    • 84948440327 scopus 로고    scopus 로고
    • Single-molecule sequencing of the dessication-Tolerant grass Oropetium thomaeum
    • VanBuren, R. et al. Single-molecule sequencing of the dessication-Tolerant grass Oropetium thomaeum. Nature 527, 508-511 (2015).
    • (2015) Nature , vol.527 , pp. 508-511
    • VanBuren, R.1
  • 14
    • 84955502827 scopus 로고    scopus 로고
    • Evaluation and validation of assembling corrected PacBio long reads for microbial genome completion via hybrid approaches
    • Lin, H. H. & Liao, Y. C. Evaluation and validation of assembling corrected PacBio long reads for microbial genome completion via hybrid approaches. PLoS One 10, e0144305 (2015).
    • (2015) PLoS One , vol.10 , pp. e0144305
    • Lin, H.H.1    Liao, Y.C.2
  • 15
    • 84913554630 scopus 로고    scopus 로고
    • One chromosome, one contig: Complete microbial genomes from long-read sequencing and assembly
    • Koren, S. & Phillipy, A. M. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110-120 (2015).
    • (2015) Curr. Opin. Microbiol , vol.23 , pp. 110-120
    • Koren, S.1    Phillipy, A.M.2
  • 16
    • 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 (2015).
    • (2015) Biomol. Detect. Quantif , vol.3 , pp. 1-8
    • Laver, T.1
  • 17
    • 84936764311 scopus 로고    scopus 로고
    • Scaffolding of a bacterial genome using MinION nanopore sequencing
    • Karlsson, E., Lärkeryd, A., Sjödin, A., Forsman, M. & Stenberg, P. Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci. Rep. 5, 11996 (2015).
    • (2015) Sci. Rep , vol.5 , pp. 11996
    • Karlsson, E.1    Lärkeryd, A.2    Sjödin, A.3    Forsman, M.4    Stenberg, P.5
  • 18
    • 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 (2015).
    • (2015) BMC Genomics , vol.16 , pp. 327
    • Madoui, M.A.1
  • 19
    • 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 (2015).
    • (2015) Genome Res , vol.25 , pp. 1750-1756
    • Goodwin, S.1
  • 20
    • 84938421951 scopus 로고    scopus 로고
    • A complete bacterial genome assembled de novo using only nanopore sequencing data
    • Loman, N. J., Quick, J. & Simpson, J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733-735 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 733-735
    • Loman, N.J.1    Quick, J.2    Simpson, J.T.3
  • 21
    • 84863651532 scopus 로고    scopus 로고
    • Hybrid error correction and de novo assembly of single-molecule sequencing reads
    • Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693-700 (2012).
    • (2012) Nat. Biotechnol , vol.30 , pp. 693-700
    • Koren, S.1
  • 23
    • 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 (2015).
    • (2015) Nat. Biotechnol , vol.33 , pp. 623-630
    • Berlin, K.1
  • 24
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 25
    • 0020036848 scopus 로고
    • Octopine Ti-plasmid deletion mutants of Agrobacterium tumefaciens with emphasis on the right side of the T-region
    • Ooms, G. et al. Octopine Ti-plasmid deletion mutants of Agrobacterium tumefaciens with emphasis on the right side of the T-region. Plasmid 7, 15-29 (1982).
    • (1982) Plasmid , vol.7 , pp. 15-29
    • Ooms, G.1
  • 26
    • 84998817133 scopus 로고    scopus 로고
    • Genome sequence of the octopine-Type agrobacterium tumefaciens strain ach5
    • e00225-00214
    • Henkel, C. V., den Dulk-Ras, A., Zhang, X. & Hooykaas, P. J. J. Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5. Genome Announc. 2, e00225-00214 (2014).
    • (2014) Genome Announc , vol.2
    • Henkel, C.V.1    Den Dulk-Ras, A.2    Zhang, X.3    Hooykaas, P.J.J.4
  • 28
    • 84881246791 scopus 로고    scopus 로고
    • Error analysis of idealized nanopore sequencing
    • O'Donnell, C. R., Wang, H. & Dunbar, W. B. Error analysis of idealized nanopore sequencing. Electrophoresis 34, 2137-2144 (2013).
    • (2013) Electrophoresis , vol.34 , pp. 2137-2144
    • O'Donnell, C.R.1    Wang, H.2    Dunbar, W.B.3
  • 29
    • 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 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 30
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 32
    • 79954553212 scopus 로고    scopus 로고
    • Improving SNP discovery by base alignment quality
    • Li, H. Improving SNP discovery by base alignment quality. Bioinformatics 27, 1157-1158 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1157-1158
    • Li, H.1
  • 34
    • 84943637090 scopus 로고    scopus 로고
    • De novo sequencing and variant calling with nanopores using PoreSeq
    • Szalay, T. & Golovchenko, J. A. De novo sequencing and variant calling with nanopores using PoreSeq. Nat. Biotechnol. 33, 1087-1091 (2015).
    • (2015) Nat. Biotechnol , vol.33 , pp. 1087-1091
    • Szalay, T.1    Golovchenko, J.A.2
  • 35
    • 84902707563 scopus 로고    scopus 로고
    • SSPACE-LongRead: Scaffolding bacterial draft genomes using long read sequence information
    • Boetzer, M. & Pirovano, W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 15, 211 (2014).
    • (2014) BMC Bioinformatics , vol.15 , pp. 211
    • Boetzer, M.1    Pirovano, W.2
  • 36
    • 84914689868 scopus 로고    scopus 로고
    • Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
    • Walker, B. J. et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).
    • (2014) PLoS One , vol.9 , pp. e112963
    • Walker, B.J.1
  • 37
    • 84976523069 scopus 로고    scopus 로고
    • Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
    • Sović, I., Križanović, K., Skala, K. & Šikić, M. Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. bioRxiv., doi: 10.1101/030437 (2015).
    • (2015) BioRxiv
    • Sović, I.1    Križanović, K.2    Skala, K.3    Šikić, M.4
  • 38
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marçais, G.1    Kingsford, C.2
  • 39
    • 0034201441 scopus 로고    scopus 로고
    • Emboss: The european molecular biology open software suite
    • Rice, P., Longden, J. & Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, J.2    Bleasby, A.3
  • 40
    • 84891813159 scopus 로고    scopus 로고
    • Application of ggplot2 to pharmacometric graphics
    • Ito, K. & Murphy, D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst. Pharmacol. 2, e79 (2013).
    • (2013) CPT Pharmacometrics Syst. Pharmacol , vol.2 , pp. e79
    • Ito, K.1    Murphy, D.2
  • 41
    • 77956519355 scopus 로고    scopus 로고
    • GenoPlotR: Comparative gene and genome visualization in R
    • Guy, L., Kultima, J. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334-2335 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2334-2335
    • Guy, L.1    Kultima, J.2    Andersson, S.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.