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Volumn , Issue , 2014, Pages 51-58

Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph

Author keywords

Bloom filter; de Bruijn graph; de novo genome assembly; paired end sequencing

Indexed keywords


EID: 84922804426     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2014.6999126     Document Type: Conference Paper
Times cited : (15)

References (35)
  • 2
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • May
    • D. R. Zerbino and E. Birney, "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs," Genome Research, vol. 18, pp. 821-829, May 2008.
    • (2008) Genome Research , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 4
    • 84857838310 scopus 로고    scopus 로고
    • Efficient de novo assembly of large genomes using compressed data structures
    • Mar
    • J. T. Simpson and R. Durbin, "Efficient de novo assembly of large genomes using compressed data structures," Genome Research, vol. 22, pp. 549-556, Mar 2012.
    • (2012) Genome Research , vol.22 , pp. 549-556
    • Simpson, J.T.1    Durbin, R.2
  • 5
    • 84874330144 scopus 로고    scopus 로고
    • SCARPA: Scaffolding reads with practical algorithms
    • Feb
    • N. Donmez and M. Brudno, "SCARPA: scaffolding reads with practical algorithms," Bioinformatics, vol. 29, pp. 428-434, Feb 2013.
    • (2013) Bioinformatics , vol.29 , pp. 428-434
    • Donmez, N.1    Brudno, M.2
  • 7
    • 0346505466 scopus 로고    scopus 로고
    • Hierarchical scaffolding with Bambus
    • Jan
    • M. Pop, D. S. Kosack, and S. L. Salzberg, "Hierarchical scaffolding with Bambus," Genome Research, vol. 14, pp. 149-159, Jan 2004.
    • (2004) Genome Research , vol.14 , pp. 149-159
    • Pop, M.1    Kosack, D.S.2    Salzberg, S.L.3
  • 9
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Nov 1
    • K. Ye, M. H. Schulz, Q. Long, R. Apweiler, and Z. Ning, "Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads," Bioinformatics, vol. 25, pp. 2865-2871, Nov 1 2009.
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 10
    • 67649580757 scopus 로고    scopus 로고
    • MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions
    • Jul
    • S. Lee, F. Hormozdiari, C. Alkan, and M. Brudno, "MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions," Nature Methods, vol. 6, pp. 473-474, Jul 2009.
    • (2009) Nature Methods , vol.6 , pp. 473-474
    • Lee, S.1    Hormozdiari, F.2    Alkan, C.3    Brudno, M.4
  • 11
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: Structural variant discovery by integrated paired-end and split-read analysis
    • Sep 15
    • T. Rausch, T. Zichner, A. Schlattl, A. M. Stuetz, V. Benes, and J. O. Korbel, "DELLY: structural variant discovery by integrated paired-end and split-read analysis," Bioinformatics, vol. 28, pp. I333-I339, Sep 15 2012.
    • (2012) Bioinformatics , vol.28 , pp. I333-I339
    • Rausch, T.1    Zichner, T.2    Schlattl, A.3    Stuetz, A.M.4    Benes, V.5    Korbel, J.O.6
  • 12
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • Nov 1
    • T. Magoc and S. L. Salzberg, "FLASH: fast length adjustment of short reads to improve genome assemblies," Bioinformatics, vol. 27, pp. 2957-63, Nov 1 2011.
    • (2011) Bioinformatics , vol.27 , pp. 2957-2963
    • Magoc, T.1    Salzberg, S.L.2
  • 13
  • 14
    • 84878338848 scopus 로고    scopus 로고
    • ELOPER: Elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly
    • Jun 1
    • D. H. Silver, S. Ben-Elazar, A. Bogoslavsky, and I. Yanai, "ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly," Bioinformatics, vol. 29, pp. 1455-1457, Jun 1 2013.
    • (2013) Bioinformatics , vol.29 , pp. 1455-1457
    • Silver, D.H.1    Ben-Elazar, S.2    Bogoslavsky, A.3    Yanai, I.4
  • 15
    • 84871481892 scopus 로고    scopus 로고
    • GapFiller: A de novo assembly approach to fill the gap within paired reads
    • Sep 7
    • F. Nadalin, F. Vezzi, and A. Policriti, "GapFiller: a de novo assembly approach to fill the gap within paired reads," Bmc Bioinformatics, vol. 13, Sep 7 2012.
    • (2012) Bmc Bioinformatics , vol.13
    • Nadalin, F.1    Vezzi, F.2    Policriti, A.3
  • 17
    • 78349238864 scopus 로고    scopus 로고
    • Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • Nov
    • S. Boisvert, F. Laviolette, and J. Corbeil, "Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies," J Comput Biol, vol. 17, pp. 1519-33, Nov 2010.
    • (2010) J Comput Biol , vol.17 , pp. 1519-1533
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 18
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Jul 15
    • H. Li and R. Durbin, "Fast and accurate short read alignment with Burrows-Wheeler transform," Bioinformatics, vol. 25, pp. 1754-60, Jul 15 2009.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 19
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome," Genome Biol, vol. 10, p. R25, 2009.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 21
    • 0014814325 scopus 로고
    • Space/time tradeoffs in hash coding with allowable errors
    • B. H. Bloom, "Space/Time Tradeoffs in Hash Coding With Allowable Errors," Communications of the Acm, vol. 13, pp. 422-&, 1970 1970.
    • (1970) Communications of the Acm , vol.13 , pp. 422
    • Bloom, B.H.1
  • 23
    • 84883784774 scopus 로고    scopus 로고
    • Space-efficient and exact de Bruijn graph representation based on a Bloom filter
    • Sep 16
    • R. Chikhi and G. Rizk, "Space-efficient and exact de Bruijn graph representation based on a Bloom filter," Algorithms for Molecular Biology, vol. 8, Sep 16 2013.
    • (2013) Algorithms for Molecular Biology , vol.8
    • Chikhi, R.1    Rizk, G.2
  • 25
    • 0022422660 scopus 로고
    • Nomenclature for incompletely specified bases in nucleic-acid sequences-recommendations 1984
    • A. Cornishbowden, "Nomenclature For Incompletely Specified Bases In Nucleic-Acid Sequences-Recommendations 1984," Nucleic Acids Research, vol. 13, pp. 3021-3030, 1985 1985.
    • (1985) Nucleic Acids Research , vol.13 , pp. 3021-3030
    • Cornishbowden, A.1
  • 26
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Mar 25
    • T. F. Smith and M. S. Waterman, "Identification of common molecular subsequences," J Mol Biol, vol. 147, pp. 195-7, Mar 25 1981.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 29
    • 84899091773 scopus 로고    scopus 로고
    • A comprehensive evaluation of assembly scaffolding tools
    • M. N. Hunt, Chris; Berriman, Matthew; Otto, Thomas D., "A comprehensive evaluation of assembly scaffolding tools," Genome Biol, vol. 15, p. R42, 2014.
    • (2014) Genome Biol , vol.15 , pp. R42
    • Hunt, M.N.1    Chris, B.2    Matthew, O.3    Thomas, D.4
  • 30
    • 84862591603 scopus 로고    scopus 로고
    • Toward almost closed genomes with GapFiller
    • M. Boetzer and W. Pirovano, "Toward almost closed genomes with GapFiller," Genome Biol, vol. 13, p. R56, 2012.
    • (2012) Genome Biol , vol.13 , pp. R56
    • Boetzer, M.1    Pirovano, W.2
  • 33
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de Bruijn graphs
    • Z. C. Iqbal, Mario; Turner, Isaac; Flicek, Paul; McVean, Gil, "De novo assembly and genotyping of variants using colored de Bruijn graphs," Nature genetics, vol. 44, p. 7, 2012.
    • (2012) Nature Genetics , vol.44 , pp. 7
    • Iqbal, Z.C.1    Mario, T.2    Isaac, F.3    Paul, M.G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.