메뉴 건너뛰기




Volumn 6, Issue 4, 2011, Pages

Comparing De Novo genome assembly: The long and short of it

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; BIOTECHNOLOGY; BRUCELLA; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; HELICOBACTER; HUMAN; NONHUMAN; QUALITY CONTROL; SEQUENCE ASSEMBLER; STANDARDIZATION; STAPHYLOCOCCUS; WOLBACHIA; Y CHROMOSOME; ALGORITHM; BACTERIAL GENOME; BIOLOGY; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENOMICS; HUMAN GENOME; METHODOLOGY; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY;

EID: 79955724657     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019175     Document Type: Article
Times cited : (82)

References (52)
  • 1
    • 77952242983 scopus 로고    scopus 로고
    • Characterization of missing human genome sequences and copy-number polymorphic insertions
    • Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, et al. (2010) Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature Methods 7: 365-371.
    • (2010) Nature Methods , vol.7 , pp. 365-371
    • Kidd, J.M.1    Sampas, N.2    Antonacci, F.3    Graves, T.4    Fulton, R.5
  • 2
  • 3
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE, (2011) Limitations of next-generation genome sequence assembly. Nature Methods 8: 61-65.
    • (2011) Nature Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 4
    • 0024135088 scopus 로고
    • A greedy approximation algorithm for constructing shortest common superstrings
    • Tarhio J, Ukkonen E, (1988) A greedy approximation algorithm for constructing shortest common superstrings. Theor Comput Sci 57: 131-145.
    • (1988) Theor Comput Sci , vol.57 , pp. 131-145
    • Tarhio, J.1    Ukkonen, E.2
  • 6
    • 0008068437 scopus 로고    scopus 로고
    • Phrap documentation
    • Available:. Accessed 2011 Apr 11
    • Green P, (1996) Phrap documentation. Available: Http://www.phrap.org/phredphrap/phrap.html. Accessed 2011 Apr 11.
    • (1996)
    • Green, P.1
  • 7
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA Sequence Assembly Program
    • Huang X, Madan A, (1999) CAP3: A DNA Sequence Assembly Program. Genome Research 9: 868-877.
    • (1999) Genome Research , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 10
    • 37249080658 scopus 로고    scopus 로고
    • Computability of models for sequence assembly
    • Springer, doi:10.1007/978-3-540-74126-8_27. Available:. Accessed 2011 Apr 11
    • Medvedev P, Georgiou K, Myers G, Brudno M, (2007) Computability of models for sequence assembly. Algorithms in Bioinformatics, Springer pp. 289-301 doi:10.1007/978-3-540-74126-8_27. Available: http://dx.doi.org/10.1007/978-3-540-74126-8_27. Accessed 2011 Apr 11.
    • (2007) Algorithms in Bioinformatics , pp. 289-301
    • Medvedev, P.1    Georgiou, K.2    Myers, G.3    Brudno, M.4
  • 11
    • 27744514080 scopus 로고    scopus 로고
    • Solving the path cover problem on circular-arc graphs by using an approximation algorithmstar
    • Hung RW, Chang MS, (2006) Solving the path cover problem on circular-arc graphs by using an approximation algorithmstar. Discrete Applied Mathematics 154: 76-105.
    • (2006) Discrete Applied Mathematics , vol.154 , pp. 76-105
    • Hung, R.W.1    Chang, M.S.2
  • 16
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
    • Hernandez D, Franois P, Farinelli L, sters M, Schrenzel J, (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Research 18: 802-809.
    • (2008) Genome Research , vol.18 , pp. 802-809
    • Hernandez, D.1    Franois, P.2    Farinelli, L.3    Sters, M.4    Schrenzel, J.5
  • 18
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
    • (2008) Genome Research , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 20
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20: 265-272.
    • (2010) Genome Research , vol.20 , pp. 265-272
    • Li, R.1    Zhu, H.2    Ruan, J.3    Qian, W.4    Fang, X.5
  • 21
    • 35948929094 scopus 로고    scopus 로고
    • SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 17: 1697-1706.
    • (2007) Genome Research , vol.17 , pp. 1697-1706
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 23
    • 62549098185 scopus 로고    scopus 로고
    • Qsra - a quality-value guided de novo short read assembler
    • Bryant D, Wong WK, Mockler T, (2009) Qsra- a quality-value guided de novo short read assembler. BMC Bioinformatics 10: 69.
    • (2009) BMC Bioinformatics , vol.10 , pp. 69
    • Bryant, D.1    Wong, W.K.2    Mockler, T.3
  • 25
    • 78651428162 scopus 로고    scopus 로고
    • Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons
    • Narzisi G, Mishra B, (2011) Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons. Bioinformatics 27: 153-160.
    • (2011) Bioinformatics , vol.27 , pp. 153-160
    • Narzisi, G.1    Mishra, B.2
  • 26
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International
    • International (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 27
    • 28944439470 scopus 로고    scopus 로고
    • Beware of mis-assembled genomes
    • Salzberg SL, Yorke JA, (2005) Beware of mis-assembled genomes. Bioinformatics 21: 4320-4321.
    • (2005) Bioinformatics , vol.21 , pp. 4320-4321
    • Salzberg, S.L.1    Yorke, J.A.2
  • 30
    • 19344378727 scopus 로고    scopus 로고
    • Phylogenomics of the reproductive parasite wolbachia pipientis wmel: A streamlined genome overrun by mobile genetic elements
    • Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, et al. (2004) Phylogenomics of the reproductive parasite wolbachia pipientis wmel: A streamlined genome overrun by mobile genetic elements. PLoS Biol 2: e69.
    • (2004) PLoS Biol , vol.2
    • Wu, M.1    Sun, L.V.2    Vamathevan, J.3    Riegler, M.4    Deboy, R.5
  • 31
    • 20144372744 scopus 로고    scopus 로고
    • Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Strain
    • Gill SR, Fouts DE, Archer GL, Mongodin EF, DeBoy RT, et al. (2005) Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Strain. J Bacteriol 187: 2426-2438.
    • (2005) J Bacteriol , vol.187 , pp. 2426-2438
    • Gill, S.R.1    Fouts, D.E.2    Archer, G.L.3    Mongodin, E.F.4    DeBoy, R.T.5
  • 32
    • 0037172403 scopus 로고    scopus 로고
    • Genome and virulence determinants of high virulence community-acquired mrsa
    • Baba T, Takeuchi F, Kuroda M, Yuzawa H, ichi Aoki K, et al. (2002) Genome and virulence determinants of high virulence community-acquired mrsa. The Lancet 359: 1819-1827.
    • (2002) The Lancet , vol.359 , pp. 1819-1827
    • Baba, T.1    Takeuchi, F.2    Kuroda, M.3    Yuzawa, H.4    Ichi Aoki, K.5
  • 33
    • 33746612926 scopus 로고    scopus 로고
    • Who ate whom? adaptive ¡italic¿helicobacter¡/italic¿ genomic changes that accompanied a host jump from early humans to large felines
    • Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, et al. (2006) Who ate whom? adaptive ¡italic¿helicobacter¡/italic¿ genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet 2: e120.
    • (2006) PLoS Genet , vol.2
    • Eppinger, M.1    Baar, C.2    Linz, B.3    Raddatz, G.4    Lanz, C.5
  • 35
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • Chaisson MJ, Pevzner PA, (2008) Short read fragment assembly of bacterial genomes. Genome Research 18: 324-330.
    • (2008) Genome Research , vol.18 , pp. 324-330
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 38
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: finding the elusive mis-assembly
    • Phillippy A, Schatz M, Pop M, (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biology 9: R55.
    • (2008) Genome Biology , vol.9
    • Phillippy, A.1    Schatz, M.2    Pop, M.3
  • 39
    • 77957995184 scopus 로고    scopus 로고
    • Revolution postponed
    • Hall SS, (2010) Revolution postponed. Scientific American pp. 60-67.
    • (2010) Scientific American , pp. 60-67
    • Hall, S.S.1
  • 40
    • 0033168288 scopus 로고    scopus 로고
    • Optical mapping and its potential for large-scale sequencing projects
    • Aston C, Mishra B, Schwartz DC, (1999) Optical mapping and its potential for large-scale sequencing projects. Trends in Biotechnology 17: 297-302.
    • (1999) Trends in Biotechnology , vol.17 , pp. 297-302
    • Aston, C.1    Mishra, B.2    Schwartz, D.C.3
  • 43
    • 0030856495 scopus 로고    scopus 로고
    • Genomics via optical mapping. ii: Ordered restriction maps
    • Anantharaman T, Mishra B, Schwartz D, (1997) Genomics via optical mapping. ii: Ordered restriction maps. J Comput Biol 4: 91-118.
    • (1997) J Comput Biol , vol.4 , pp. 91-118
    • Anantharaman, T.1    Mishra, B.2    Schwartz, D.3
  • 44
    • 26444494195 scopus 로고    scopus 로고
    • Genomics via optical mapping iv: Sequence validation via optical map matching
    • Technical report, New York University, New York, NY, USA
    • Antoniotti M, Anantharaman T, Paxia S, Mishra B, (2001) Genomics via optical mapping iv: Sequence validation via optical map matching. Technical report, New York University, New York, NY, USA.
    • (2001)
    • Antoniotti, M.1    Anantharaman, T.2    Paxia, S.3    Mishra, B.4
  • 48
    • 78349238864 scopus 로고    scopus 로고
    • Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • Boisvert S, Laviolette F, Corbeil J, (2010) Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of Computational Biology 17: 1519-1533.
    • (2010) Journal of Computational Biology , vol.17 , pp. 1519-1533
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 49
    • 77949511368 scopus 로고    scopus 로고
    • Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
    • Zerbino DR, McEwen GK, Margulies EH, Birney E, (2009) Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE 4: e8407.
    • (2009) PLoS ONE , vol.4
    • Zerbino, D.R.1    McEwen, G.K.2    Margulies, E.H.3    Birney, E.4
  • 50
    • 78651433774 scopus 로고    scopus 로고
    • PE-Assembler: de novo assembler using short paired-end reads
    • Ariyaratne PN, Sung WK, (2011) PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 27: 167-174.
    • (2011) Bioinformatics , vol.27 , pp. 167-174
    • Ariyaratne, P.N.1    Sung, W.K.2
  • 51


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.