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Volumn 30, Issue 1, 2014, Pages 40-49

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SOFTWARE; STAPHYLOCOCCUS AUREUS; ARTICLE; CHROMOSOME MAP; COMPUTER PROGRAM; METHODOLOGY;

EID: 84891349481     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt590     Document Type: Article
Times cited : (47)

References (27)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0037172403 scopus 로고    scopus 로고
    • Genome and virulence determinants of high virulence community-acquired MRSA
    • Baba, T. et al. (2002) Genome and virulence determinants of high virulence community-acquired MRSA. Lancet, 359, 1819-1827.
    • (2002) Lancet , vol.359 , pp. 1819-1827
    • Baba, T.1
  • 3
    • 84862591603 scopus 로고    scopus 로고
    • Toward almost closed genomes with GapFiller
    • Boetzer, M. and Pirovano, W. (2012) Toward almost closed genomes with GapFiller. Genome Biol., 13, R56.
    • (2012) Genome Biol. , vol.13
    • Boetzer, M.1    Pirovano, W.2
  • 4
    • 78349238864 scopus 로고    scopus 로고
    • Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • Boisvert, S. et al. (2010) Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol., 17, 1519-1533.
    • (2010) J. Comput. Biol. , vol.17 , pp. 1519-1533
    • Boisvert, S.1
  • 5
    • 84866440990 scopus 로고    scopus 로고
    • Telescoper: De novo assembly of highly repetitive regions
    • Bresler, M. et al. (2012) Telescoper: de novo assembly of highly repetitive regions. Bioinformatics., 28, i311-i317.
    • (2012) Bioinformatics. , vol.28
    • Bresler, M.1
  • 6
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Butler, J. et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1
  • 7
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA, 108, 1513-1518.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 1513-1518
    • Gnerre, S.1
  • 8
    • 0032524384 scopus 로고    scopus 로고
    • Analyzing genomes with cumulative skew diagrams
    • Grigoriev, A. (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res., 26, 2286-2290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 9
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich, A. et al. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075.
    • (2013) Bioinformatics , vol.29 , pp. 1072-1075
    • Gurevich, A.1
  • 10
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
    • Hernandez, D. et al. (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res., 18, 802-809.
    • (2008) Genome Res. , vol.18 , pp. 802-809
    • Hernandez, D.1
  • 11
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 12
    • 0035925904 scopus 로고    scopus 로고
    • Whole genome sequencing of meticillin-resistant Staphylococcus aureus
    • Kuroda, M. et al. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet, 357, 1225-1240.
    • (2001) Lancet , vol.357 , pp. 1225-1240
    • Kuroda, M.1
  • 13
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
    • (2004) Genome Biol. , vol.5
    • Kurtz, S.1
  • 14
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics., 25, 1754-1760.
    • (2009) Bioinformatics. , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 15
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • Li, H. et al. (2009) The sequence alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 16
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272.
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1
  • 17
    • 27544497879 scopus 로고    scopus 로고
    • The fragment assembly string graph
    • Myers, E.W. (2005) The fragment assembly string graph. Bioinformatics, 21 (Suppl. 2), ii79-ii85.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Myers, E.W.1
  • 18
    • 0035232164 scopus 로고    scopus 로고
    • Fragment assembly with double-barreled data
    • Pevzner, P.A. and Tang, H. (2001) Fragment assembly with double-barreled data. Bioinformatics, 17 (Suppl. 1), S225-S233.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pevzner, P.A.1    Tang, H.2
  • 19
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner, P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-9753.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9748-9753
    • Pevzner, P.A.1
  • 20
    • 4644275238 scopus 로고    scopus 로고
    • De novo repeat classification and fragment assembly
    • Pevzner, P.A. et al. (2004) De novo repeat classification and fragment assembly. Genome Res., 14, 1786-1796.
    • (2004) Genome Res. , vol.14 , pp. 1786-1796
    • Pevzner, P.A.1
  • 21
    • 67449095888 scopus 로고    scopus 로고
    • Genome assembly reborn: Recent computational challenges
    • Pop, M. (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform., 10, 354-366.
    • (2009) Brief Bioinform. , vol.10 , pp. 354-366
    • Pop, M.1
  • 22
    • 84868327508 scopus 로고    scopus 로고
    • Finished bacterial genomes from shotgun sequence data
    • Ribeiro, F. et al. (2012) Finished bacterial genomes from shotgun sequence data. Genome Res., 22, 2270-2277.
    • (2012) Genome Res. , vol.22 , pp. 2270-2277
    • Ribeiro, F.1
  • 23
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 24
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater, G.S. and Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 25
    • 77950658346 scopus 로고    scopus 로고
    • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    • Tsai, I.J. et al. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol., 11, R41.
    • (2010) Genome Biol. , vol.11
    • Tsai, I.J.1
  • 26
    • 84865022311 scopus 로고    scopus 로고
    • Primer3-new capabilities and interfaces
    • Untergasser, A. et al. (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res., 40, e115.
    • (2012) Nucleic Acids Res. , vol.40
    • Untergasser, A.1
  • 27
    • 79953854485 scopus 로고    scopus 로고
    • Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
    • Wetzel, J. et al. (2011) Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics, 12, 95.
    • (2011) BMC Bioinformatics , vol.12 , pp. 95
    • Wetzel, J.1


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