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Volumn 30, Issue 12, 2014, Pages

ExSPAnder: A universal repeat resolver for DNA fragment assembly

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 84902509478     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu266     Document Type: Article
Times cited : (93)

References (20)
  • 1
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
    • (2012) J. Comput. Biol. , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 2
    • 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
  • 3
    • 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, 311-317.
    • (2012) Bioinformatics , vol.28 , pp. 311-317
    • Bresler, M.1
  • 4
    • 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
  • 5
    • 80054732674 scopus 로고    scopus 로고
    • Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
    • Chitsaz, H. et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol., 29, 915-921.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 915-921
    • Chitsaz, H.1
  • 6
    • 80755159050 scopus 로고    scopus 로고
    • How to apply de Bruijn graphs to genome assembly
    • Compeau, F. et al. (2011) How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol., 29, 987-991.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 987-991
    • Compeau, F.1
  • 7
    • 33644659999 scopus 로고    scopus 로고
    • Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus
    • Diep, B. et al. (2006) Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet, 367, 731-739.
    • (2006) Lancet , vol.367 , pp. 731-739
    • Diep, B.1
  • 8
    • 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
  • 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
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with bowtie 2
    • Langmead, B. and Salzberg, S. (2012) Fast gapped-read alignment with bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.2
  • 11
    • 80054039848 scopus 로고    scopus 로고
    • Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10)
    • Lapidus, A. et al. (2009) Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Standards Genomic Sci., 1, 3-11.
    • (2009) Standards Genomic Sci. , vol.1 , pp. 3-11
    • Lapidus, A.1
  • 12
    • 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
  • 13
    • 84885626275 scopus 로고    scopus 로고
    • Assembling single-cell genomes and mini-metagenomes from chimeric MDA products
    • Nurk, S. et al. (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol., 20, 1-24.
    • (2013) J. Comput. Biol. , vol.20 , pp. 1-24
    • Nurk, S.1
  • 14
    • 80955139667 scopus 로고    scopus 로고
    • Paired de bruijn graphs: A novel approach for incorporating mate pair information into genome assemblers
    • Medvedev, P. et al. (2011) Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J. Comput. Biol., 18, 1625-1634.
    • (2011) J. Comput. Biol. , vol.18 , pp. 1625-1634
    • Medvedev, P.1
  • 15
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metage-nomic sequencing data with highly uneven depth
    • Peng, Y. et al. (2012) IDBA-UD: a de novo assembler for single-cell and metage-nomic sequencing data with highly uneven depth. Bioinformatics, 28, 1-8.
    • (2012) Bioinformatics , vol.28 , pp. 1-8
    • Peng, Y.1
  • 16
    • 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
  • 17
    • 84874192171 scopus 로고    scopus 로고
    • Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly
    • Pham, S. et al. (2013) Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. J. Comput. Biol., 20, 259-371.
    • (2013) J. Comput. Biol. , vol.20 , pp. 259-371
    • Pham, S.1
  • 18
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J. 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.1
  • 19
    • 84866643142 scopus 로고    scopus 로고
    • From de Bruijn graphs to rectangle graphs for genome assembly " in Workshop on Algorithms in Bioinformatics 2012
    • Vyahhi, N. et al. (2012) From de Bruijn graphs to rectangle graphs for genome assembly, " in Workshop on Algorithms in Bioinformatics 2012. Lecture Notes Comput Sci, 7534, 200-212.
    • (2012) Lecture Notes Comput Sci , vol.7534 , pp. 200-212
    • Vyahhi, N.1
  • 20
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.