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Volumn 15, Issue 1, 2014, Pages

PBHoney: Identifying genomic variants via long-read discordance and interrupted mapping

Author keywords

PacificBiosciences; Sequencing; Structural variation

Indexed keywords

BIODIVERSITY; DNA SEQUENCES; ESCHERICHIA COLI;

EID: 84903895383     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-180     Document Type: Article
Times cited : (109)

References (24)
  • 2
    • 80052729161 scopus 로고    scopus 로고
    • Copy-number variations, noncoding sequences, and human phenotypes
    • Klopocki E, Mundlos S. Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev Genomics Hum Genet 2011, 12:53-72.
    • (2011) Annu Rev Genomics Hum Genet , vol.12 , pp. 53-72
    • Klopocki, E.1    Mundlos, S.2
  • 3
    • 84856244406 scopus 로고    scopus 로고
    • Implications of gene copy-number variation in health and diseases
    • Almal SH, Padh H. Implications of gene copy-number variation in health and diseases. J Hum Genet 2012, 57(1):6-13.
    • (2012) J Hum Genet , vol.57 , Issue.1 , pp. 6-13
    • Almal, S.H.1    Padh, H.2
  • 4
    • 84883536382 scopus 로고    scopus 로고
    • The growing importance of CNVs: new insights for detection and clinical interpretation
    • Macé A
    • Valsesia A, Beckmann JS, . Macé A The growing importance of CNVs: new insights for detection and clinical interpretation. Front Gene 2013, 4:92. Macé A.
    • (2013) Front Gene , vol.4 , pp. 92
    • Valsesia, A.1    Beckmann, J.S.2
  • 5
    • 84885188208 scopus 로고    scopus 로고
    • Impacts of variation in the human genome on gene regulation
    • Haraksingh RR, Snyder MP. Impacts of variation in the human genome on gene regulation. J Mol Biol 2013, 425(21):3970-3977.
    • (2013) J Mol Biol , vol.425 , Issue.21 , pp. 3970-3977
    • Haraksingh, R.R.1    Snyder, M.P.2
  • 6
    • 84883851164 scopus 로고    scopus 로고
    • Comparing a few SNP calling algorithms using low-coverage sequencing data
    • Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC, Bioinformatics 2013, 14(1):274.
    • (2013) BMC, Bioinformatics , vol.14 , Issue.1 , pp. 274
    • Yu, X.1    Sun, S.2
  • 7
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: structural variant discovery by integrated paired-end and split-read analysis
    • Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 2012, 28(18):333-339.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 333-339
    • Rausch, T.1    Zichner, T.2    Schlattl, A.3    Stütz, A.M.4    Benes, V.5    Korbel, J.O.6
  • 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
    • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25(21):2865-2871.
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 12
    • 84896448861 scopus 로고    scopus 로고
    • A survey of tools for variant analysis of next-generation genome sequencing data
    • doi:10.1093/bib/bbs086, First published online: January 21, 2013
    • Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform 2014, 15(2):256-278. http://bib.oxfordjournals.org/content/15/2/256 doi:10.1093/bib/bbs086 First published online: January 21, 2013.
    • (2014) Brief Bioinform , vol.15 , Issue.2 , pp. 256-278
    • Pabinger, S.1    Dander, A.2    Fischer, M.3    Snajder, R.4    Sperk, M.5    Efremova, M.6    Krabichler, B.7    Speicher, M.R.8    Zschocke, J.9    Trajanoski, Z.10
  • 13
    • 84866266717 scopus 로고    scopus 로고
    • Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
    • Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012, 13:238.
    • (2012) BMC Bioinformatics , vol.13 , pp. 238
    • Chaisson, M.J.1    Tesler, G.2
  • 14
    • 77952855601 scopus 로고    scopus 로고
    • Structural variation analysis with strobe reads
    • doi:10.1093/bioinformatics/btq153 First published online: April 8, 2010
    • Ritz A, Bashir A, Benjamin RJ. Structural variation analysis with strobe reads. Bioinformatics 2010, 26(10):1291-1298. http://bioinformatics.oxfordjournals.org/content/26/10/1291 doi:10.1093/bioinformatics/btq153 First published online: April 8, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.10 , pp. 1291-1298
    • Ritz, A.1    Bashir, A.2    Benjamin, R.J.3
  • 15
    • 84867316247 scopus 로고    scopus 로고
    • Yaha: fast and flexible long-read alignment with optimal breakpoint detection
    • doi:10.1093/bioinformatics/bts456 First published online: July 24, 2012
    • Faust GG, Hall IM. Yaha: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics 2012, 28(19):2417-2424. http://bioinformatics.oxfordjournals.org/content/28/19/2417.full doi:10.1093/bioinformatics/bts456 First published online: July 24, 2012.
    • (2012) Bioinformatics , vol.28 , Issue.19 , pp. 2417-2424
    • Faust, G.G.1    Hall, I.M.2
  • 16
    • 68549104404 scopus 로고    scopus 로고
    • The sequence Alignment/Map format and SAMtools
    • 1000 Genome Project Data Processing Subgroup
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 1000 Genome Project Data Processing Subgroup.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 17
    • 84871392152 scopus 로고    scopus 로고
    • Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile x gene
    • Published in Advance October 11, 2012, doi:10.1101/gr.141705.112
    • Loomis EW, Eid JS, Peluso P, Yin J, Hickey L, Rank D, McCalmon S, Hagerman RJ, Tassone F, Hagerman PJ. Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile x gene. Genome Res 2012, 23:121-128. http://genome.cshlp.org/content/23/1/121.full Published in Advance October 11, 2012, doi:10.1101/gr.141705.112.
    • (2012) Genome Res , vol.23 , pp. 121-128
    • Loomis, E.W.1    Eid, J.S.2    Peluso, P.3    Yin, J.4    Hickey, L.5    Rank, D.6    McCalmon, S.7    Hagerman, R.J.8    Tassone, F.9    Hagerman, P.J.10
  • 21
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27(2):573-580.
    • (1999) Nucleic Acids Res , vol.27 , Issue.2 , pp. 573-580
    • Benson, G.1
  • 22
    • 0021913632 scopus 로고
    • The invertible p-DNA segment in the chromosome of escherichia coli
    • Plasterk RH, van de Putte P. The invertible p-DNA segment in the chromosome of escherichia coli. EMBO J 1985, 4(1):237-242.
    • (1985) EMBO J , vol.4 , Issue.1 , pp. 237-242
    • Plasterk, R.H.1    van de Putte, P.2
  • 23
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003, 100(20):11484-11489.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.20 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5


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