메뉴 건너뛰기




Volumn 9, Issue 8, 2014, Pages

Solving the problem of comparing whole bacterial genomes across different sequencing platforms

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; BACTERIAL DNA;

EID: 84905843066     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104984     Document Type: Article
Times cited : (614)

References (24)
  • 1
    • 84873809749 scopus 로고    scopus 로고
    • Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response
    • Available : Accessed 27 February 2014
    • Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, et al. (2012) Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg Infect Dis 18: e1. Available : http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3559169&tool=pmcentrez&rendertype=abstract. Accessed 27 February 2014.
    • (2012) Emerg Infect Dis , vol.18
    • Aarestrup, F.M.1    Brown, E.W.2    Detter, C.3    Gerner-Smidt, P.4    Gilmour, M.W.5
  • 2
    • 84865231395 scopus 로고    scopus 로고
    • Transforming clinical microbiology with bacterial genome sequencing
    • Available: Accessed 20 February 2014
    • Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13: 601-612. Available: http://www.ncbi.nlm.nih.gov/pubmed/22868263. Accessed 20 February 2014.
    • (2012) Nat Rev Genet , vol.13 , pp. 601-612
    • Didelot, X.1    Bowden, R.2    Wilson, D.J.3    Peto, T.E.4    Crook, D.W.5
  • 3
    • 84866148001 scopus 로고    scopus 로고
    • Routine use of microbial whole genome sequencing in diagnostic and public health microbiology
    • Available: Accessed 24 February 2014
    • Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, et al. (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8: e1002824. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3410874&tool= pmcentrez&rendertype=abstract. Accessed 24 February 2014.
    • (2012) PLoS Pathog , vol.8
    • Köser, C.U.1    Ellington, M.J.2    Cartwright, E.J.P.3    Gillespie, S.H.4    Brown, N.M.5
  • 4
    • 84872515273 scopus 로고    scopus 로고
    • Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: A descriptive study
    • Available : Accessed 27 February 2014
    • Harris SR, Cartwright EJP, Török ME, Holden MTG, Brown NM, et al. (2013) Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 13: 130-136. Available : http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=3556525&tool=pmcentrez&rendertype=abstract. Accessed 27 February 2014.
    • (2013) Lancet Infect Dis , vol.13 , pp. 130-136
    • Harris, S.R.1    Cartwright, E.J.P.2    Török, M.E.3    Holden, M.T.G.4    Brown, N.M.5
  • 5
    • 84863242652 scopus 로고    scopus 로고
    • Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
    • Available: Accessed 25 May 2012
    • Price L, Stegger M, Hasman H, Aziz M, Larsen J (2012) Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock. MBio 3: 1-6. Available: http://mbio.asm.org/content/3/1/e00305-11. short. Accessed 25 May 2012.
    • (2012) MBio , vol.3 , pp. 1-6
    • Price, L.1    Stegger, M.2    Hasman, H.3    Aziz, M.4    Larsen, J.5
  • 6
    • 84905849485 scopus 로고    scopus 로고
    • Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
    • Available: Accessed 27 February 2014
    • Young B, Golubchik T (2012) Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc ... Available: http://www.pnas.org/content/109/12/4550.short. Accessed 27 February 2014.
    • (2012) Proc...
    • Young, B.1    Golubchik, T.2
  • 7
    • 80052597651 scopus 로고    scopus 로고
    • Population genetics of Vibrio cholerae from Nepal in 2010: Evidence on the origin of the Haitian outbreak
    • Available: Accessed 27 February 2014
    • Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS, et al. (2011) Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio 2: 1-6. Available: http://mbio.asm.org/ content/2/4/e00157-11.short. Accessed 27 February 2014.
    • (2011) MBio , vol.2 , pp. 1-6
    • Hendriksen, R.S.1    Price, L.B.2    Schupp, J.M.3    Gillece, J.D.4    Kaas, R.S.5
  • 8
    • 79960609901 scopus 로고    scopus 로고
    • Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology
    • Available: Accessed 2014 February 27
    • Mellmann A, Harmsen D, Cummings C, Zentz EB, Leopold SR, et al. (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6: e22751. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3140518&tool=pmcentrez&rendertype=abstract. Accessed 2014 February 27.
    • (2011) PLoS One , vol.6
    • Mellmann, A.1    Harmsen, D.2    Cummings, C.3    Zentz, E.B.4    Leopold, S.R.5
  • 9
    • 84872513471 scopus 로고    scopus 로고
    • Wholegenome sequencing to delineate Mycobacterium tuberculosis outbreaks: A retrospective observational study
    • Available: Accessed 2014 February 22
    • Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, et al. (2013) Wholegenome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13: 137-146. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3556524&tool= pmcentrez&rendertype=abstract. Accessed 2014 February 22.
    • (2013) Lancet Infect Dis , vol.13 , pp. 137-146
    • Walker, T.M.1    Ip, C.L.C.2    Harrell, R.H.3    Evans, J.T.4    Kapatai, G.5
  • 10
    • 84875265483 scopus 로고    scopus 로고
    • Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
    • Available: Accessed 2014 February 25
    • Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, et al. (2013) Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68: 771-777. Available: http://www.ncbi.nlm.nih.gov/pubmed/ 23233485. Accessed 2014 February 25.
    • (2013) J Antimicrob Chemother , vol.68 , pp. 771-777
    • Zankari, E.1    Hasman, H.2    Kaas, R.S.3    Seyfarth, A.M.4    Agersø, Y.5
  • 11
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • Available: Accessed 2014 February 20
    • Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32. Available: http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid=2691003&tool=pmcentrez&rendertype= abstract. Accessed 2014 February 20.
    • (2009) Genome Biol , vol.10
    • Harismendy, O.1    Ng, P.C.2    Strausberg, R.L.3    Wang, X.4    Stockwell, T.B.5
  • 12
    • 84855566198 scopus 로고    scopus 로고
    • Performance comparison of whole-genome sequencing platforms
    • Available: Accessed 2014 February 27
    • Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, et al. (2012) Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 30: 78-82. Available: http://www.ncbi.nlm.nih.gov/pubmed/22178993. Accessed 2014 February 27.
    • (2012) Nat Biotechnol , vol.30 , pp. 78-82
    • Lam, H.Y.K.1    Clark, M.J.2    Chen, R.3    Chen, R.4    Natsoulis, G.5
  • 13
    • 84873560054 scopus 로고    scopus 로고
    • Comparison of sequencing platforms for single nucleotide variant calls in a human sample
    • Available: Accessed 2014 February 19
    • Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, et al. (2013) Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One 8: e55089. Available: http://www.pubmedcentral.nih.gov/ articlerender.fcgi?artid=3566181&tool=pmcentrez&rendertype=abstract. Accessed 2014 February 19.
    • (2013) PLoS One , vol.8
    • Ratan, A.1    Miller, W.2    Guillory, J.3    Stinson, J.4    Seshagiri, S.5
  • 14
    • 84878825544 scopus 로고    scopus 로고
    • Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies
    • Available: Accessed 2014 January 23
    • Rieber N, Zapatka M, Lasitschka B, Jones D, Northcott P, et al. (2013) Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies. PLoS One 8: e66621. Available: http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid=3679043&tool= pmcentrez&rendertype=abstract. Accessed 2014 January 23.
    • (2013) PLoS One , vol.8
    • Rieber, N.1    Zapatka, M.2    Lasitschka, B.3    Jones, D.4    Northcott, P.5
  • 15
    • 79956066785 scopus 로고    scopus 로고
    • Comparison of sequence reads obtained from three next-generation sequencing platforms
    • Available: Accessed 2014 February 27
    • Suzuki S, Ono N, Furusawa C, Ying B-W, Yomo T (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One 6: e19534. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=3096631&tool=pmcentrez&rendertype=abstract. Accessed 2014 February 27.
    • (2011) PLoS One , vol.6
    • Suzuki, S.1    Ono, N.2    Furusawa, C.3    Ying, B.-W.4    Yomo, T.5
  • 16
    • 84877266636 scopus 로고    scopus 로고
    • Updating benchtop sequencing performance comparison
    • Available
    • Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, et al. (2013) Updating benchtop sequencing performance comparison. Nat Biotechnol 31: 296. Available: http://www.ncbi.nlm.nih.gov/pubmed/23563422.
    • (2013) Nat Biotechnol , vol.31 , pp. 296
    • Jünemann, S.1    Sedlazeck, F.J.2    Prior, K.3    Albersmeier, A.4    John, U.5
  • 17
    • 84862792042 scopus 로고    scopus 로고
    • High resolution clustering of Salmonella enterica serovar Montevideo strains using a nextgeneration sequencing approach
    • Available: Accessed 2014 February 21
    • Allard MW, Luo Y, Strain E, Li C, Keys CE, et al. (2012) High resolution clustering of Salmonella enterica serovar Montevideo strains using a nextgeneration sequencing approach. BMC Genomics 13: 32. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3368722&tool= pmcentrez&rendertype=abstract. Accessed 2014 February 21.
    • (2012) BMC Genomics , vol.13 , pp. 32
    • Allard, M.W.1    Luo, Y.2    Strain, E.3    Li, C.4    Keys, C.E.5
  • 18
    • 84895096959 scopus 로고    scopus 로고
    • Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
    • Available: Accessed 2014 February 5
    • Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM (2014) Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica. PLoS One 9: e87991. Available: http://dx.plos.org/10.1371/journal. pone.0087991. Accessed 2014 February 5.
    • (2014) PLoS One , vol.9
    • Leekitcharoenphon, P.1    Nielsen, E.M.2    Kaas, R.S.3    Lund, O.4    Aarestrup, F.M.5
  • 19
    • 84878802119 scopus 로고    scopus 로고
    • snpTree - A web-server to identify and construct SNP trees from whole genome sequence data
    • Available: Accessed 2014 January 21
    • Leekitcharoenphon P, Kaas RS, Thomsen MCF, Friis C, Rasmussen S, et al. (2012) snpTree-a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics 13 Suppl 7: S6. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3521233&tool= pmcentrez&rendertype=abstract. Accessed 2014 January 21.
    • (2012) BMC Genomics , vol.13 , Issue.SUPPL. 7
    • Leekitcharoenphon, P.1    Kaas, R.S.2    Thomsen, M.C.F.3    Friis, C.4    Rasmussen, S.5
  • 20
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Available: Accessed 2014 November 7
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705234&tool= pmcentrez&rendertype=abstract. Accessed 2014 November 7.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 21
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Available: Accessed 2013 December 12
    • Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2832824&tool= pmcentrez&rendertype=abstract. Accessed 2013 December 12.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 22
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Available : Accessed 2013 December 11
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. Availabl e : http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 2723002&tool=pmcentrez&rendertype=abstract. Accessed 2013 December 11.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5
  • 23
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximumlikelihood trees for large alignments
    • Available: Accessed 2011 July 28
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS One 5: e9490. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2835736&tool= pmcentrez&rendertype=abstract. Accessed 2011 July 28.
    • (2010) PLoS One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 24
    • 84899573966 scopus 로고    scopus 로고
    • Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli
    • Available : Accessed 2014 May 27
    • Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, et al. (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52: 1501-1510. Availabl e : http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3993690&tool=pmcentrez&rendertype=abstract. Accessed 2014 May 27.
    • (2014) J Clin Microbiol , vol.52 , pp. 1501-1510
    • Joensen, K.G.1    Scheutz, F.2    Lund, O.3    Hasman, H.4    Kaas, R.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.