메뉴 건너뛰기




Volumn 30, Issue 9, 2014, Pages 1228-1235

Exploring genome characteristics and sequence quality without a reference

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENOME; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; NUCLEOTIDE SEQUENCE;

EID: 84897108483     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu023     Document Type: Article
Times cited : (116)

References (29)
  • 1
    • 84991528460 scopus 로고    scopus 로고
    • Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species
    • Bradnam, K.R. et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2, 10.
    • (2013) GigaScience , vol.2 , pp. 10
    • Bradnam, K.R.1
  • 2
    • 84891349005 scopus 로고    scopus 로고
    • Informed and automated k-mer size selection for genome assembly
    • Chikhi, R. and Medvedev, P. (2014) Informed and automated k-mer size selection for genome assembly. Bioinformatics, 30 (1), 31-37.
    • (2014) Bioinformatics , vol.30 , Issue.1 , pp. 31-37
    • Chikhi, R.1    Medvedev, P.2
  • 4
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
    • Dohm, J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1
  • 7
    • 84871070794 scopus 로고    scopus 로고
    • An alphabet-friendly FM-index
    • In: Apostolico, A. and Melucci, M. (eds) of Lecture Notes in Computer Science Springer, Berlin Heidelberg.
    • Ferragina, P. et al. (2004) An alphabet-friendly FM-index. In: Apostolico, A. and Melucci, M. (eds) String Processing and Information Retrieval, Vol. 3246 of Lecture Notes in Computer Science, pp. 150-160. Springer, Berlin Heidelberg.
    • (2004) String Processing and Information Retrieval , vol.3246 , pp. 150-160
    • Ferragina, P.1
  • 8
    • 71049176982 scopus 로고    scopus 로고
    • Genome 10K: A proposal to obtain Whole-Genome sequence for 10000 vertebrate species
    • Genome 10K Community of Scientists.
    • Springer, Berlin Heidelberg. Genome 10K Community of Scientists. (2009) Genome 10K: A proposal to obtain Whole-Genome sequence for 10000 vertebrate species. J. Heredity, 100, 659-674.
    • (2009) J. Heredity , vol.100 , pp. 659-674
  • 9
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau, A. et al. (1996) Life with 6000 genes. Science (New York, N.Y.), 274, 546-567.
    • (1996) Science (New York, N.Y.) , vol.274 , pp. 546-567
    • Goffeau, A.1
  • 10
    • 84869876659 scopus 로고    scopus 로고
    • The effect of strand bias in illumina short-read sequencing data
    • Guo, Y. et al. (2012) The effect of strand bias in illumina short-read sequencing data. BMC Genomics, 13, 666.
    • (2012) BMC Genomics , vol.13 , pp. 666
    • Guo, Y.1
  • 11
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de bruijn graphs
    • Iqbal, Z. et al. (2012) De novo assembly and genotyping of variants using colored de bruijn graphs. Nat. Genet., 44, 226-232.
    • (2012) Nat. Genet. , vol.44 , pp. 226-232
    • Iqbal, Z.1
  • 12
    • 84864044436 scopus 로고    scopus 로고
    • A platform-Independent method for detecting errors in metagenomic sequencing data: DRISEE
    • Keegan, K.P. et al. (2012) A platform-Independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput. Biol., 8, e1002541.
    • (2012) PLoS Comput. Biol. , vol.8
    • Keegan, K.P.1
  • 13
    • 78649358717 scopus 로고    scopus 로고
    • Quake: Quality-aware detection and correction of sequencing errors
    • Kelley, D. et al. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11 (11), R116.
    • (2010) Genome Biol. , vol.11 , Issue.11
    • Kelley, D.1
  • 14
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford, C. et al. (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinform., 11, 21.
    • (2010) BMC Bioinform. , vol.11 , pp. 21
    • Kingsford, C.1
  • 15
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (GC)-biased genomes
    • Kozarewa, I. et al. (2009) Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (GC)-biased genomes. Nat. Methods, 6, 291-295.
    • (2009) Nat. Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1
  • 16
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • Lander, E.S. and Waterman, M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 17
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and de novo assembly of the giant panda genome
    • Li, R. et al. (2009) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
    • (2009) Nature , vol.463 , pp. 311-317
    • Li, R.1
  • 18
    • 80052226692 scopus 로고    scopus 로고
    • Sequence-specific error profile of illumina sequencers
    • Nakamura, K. et al. (2011) Sequence-specific error profile of illumina sequencers. Nucleic Acids Res., 39, e90.
    • (2011) Nucleic Acids Res. , vol.39
    • Nakamura, K.1
  • 19
    • 84865176493 scopus 로고    scopus 로고
    • Scaling metagenome sequence assembly with probabilistic de bruijn graphs
    • Pell, J. et al. (2012) Scaling metagenome sequence assembly with probabilistic de bruijn graphs. Proc. Natl Acad. Sci. USA, 109, 13272-13277.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 13272-13277
    • Pell, J.1
  • 20
    • 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
  • 21
    • 84878234942 scopus 로고    scopus 로고
    • Characterizing and measuring bias in sequence data
    • Ross, M. et al. (2013) Characterizing and measuring bias in sequence data. Genome Biol., 14, R51.
    • (2013) Genome Biol. , vol.14
    • Ross, M.1
  • 22
    • 77958453970 scopus 로고    scopus 로고
    • Reference-Free validation of short read data
    • Schroder, J. et al. (2010) Reference-Free validation of short read data. PLoS ONE, 5, e12681.
    • (2010) PLoS ONE , vol.5
    • Schroder, J.1
  • 23
    • 84857838310 scopus 로고    scopus 로고
    • Efficient de novo assembly of large genomes using compressed data structures
    • Simpson, J.T. and Durbin, R. (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556.
    • (2012) Genome Res. , vol.22 , pp. 549-556
    • Simpson, J.T.1    Durbin, R.2
  • 24
    • 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
  • 25
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • The Potato Genome Sequencing Consortium. (2011) Genome sequence and analysis of the tuber crop potato. Nature, 475, 189-195.
    • (2011) Nature , vol.475 , pp. 189-195
  • 26
    • 84879446930 scopus 로고    scopus 로고
    • Estimation of sequencing error rates in short reads
    • Wang, X.V. et al. (2012) Estimation of sequencing error rates in short reads. BMC Bioinform., 13, 185.
    • (2012) BMC Bioinform. , vol.13 , pp. 185
    • Wang, X.V.1
  • 27
    • 0030950735 scopus 로고    scopus 로고
    • Human Whole-Genome shotgunsequencing
    • Weber, J.L. and Myers, E.W. (1997) Human Whole-Genome shotgunsequencing. Genome Res., 7, 401-409.
    • (1997) Genome Res. , vol.7 , pp. 401-409
    • Weber, J.L.1    Myers, E.W.2
  • 28
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de bruijn graphs
    • Zerbino, D.R. and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de bruijn graphs. Genome Res., 18, 821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 29
    • 84867088834 scopus 로고    scopus 로고
    • The oyster genome reveals stress adaptation and complexity of shell formation
    • Zhang, G. et al. (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490, 49-54.
    • (2012) Nature , vol.490 , pp. 49-54
    • Zhang, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.