메뉴 건너뛰기




Volumn 7534 LNBI, Issue , 2012, Pages 314-325

FinIS: Improved in silico finishing using an exact quadratic programming formulation

Author keywords

Finishing; Genome Assembly; Graph Algorithms; Quadratic Programming

Indexed keywords

ASSEMBLY SOLUTION; BLACK BOXES; EXACT SOLUTION; EXECUTABLES; FORMAL DEFINITION; GENOME ASSEMBLY; GRAPH ALGORITHMS; IN-SILICO; OPTIMAL SOLUTIONS; PRECISION AND RECALL; SIMULATED DATASETS; SOURCE CODES;

EID: 84866721437     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_25     Document Type: Conference Paper
Times cited : (23)

References (28)
  • 1
    • 79961181124 scopus 로고    scopus 로고
    • Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
    • Li, Y., Zheng, H., Luo, R., et al.: Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology 29, 6723-6730 (2011)
    • (2011) Nature Biotechnology , vol.29 , pp. 6723-6730
    • Li, Y.1    Zheng, H.2    Luo, R.3
  • 2
    • 70350664649 scopus 로고    scopus 로고
    • De novo transcriptome assembly with ABySS
    • Birol, I., Jackman, S.D., Nielsen, C.B., et al.: De novo transcriptome assembly with ABySS. Bioinformatics 25(21), 2872-2877 (2009)
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2872-2877
    • Birol, I.1    Jackman, S.D.2    Nielsen, C.B.3
  • 3
    • 33750431080 scopus 로고    scopus 로고
    • Symbiosis insights through metagenomic analysis of a microbial consortium
    • Woyke, T., Teeling, H., Ivanova, N.N., et al.: Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950-955 (2006)
    • (2006) Nature , vol.443 , pp. 950-955
    • Woyke, T.1    Teeling, H.2    Ivanova, N.N.3
  • 4
    • 79952108717 scopus 로고    scopus 로고
    • Sequencing and genome assembly using next-generation technologies
    • Nagarajan, N., Pop, M.: Sequencing and genome assembly using next-generation technologies. Methods in Molecular Biology 673, 1-17 (2010)
    • (2010) Methods in Molecular Biology , vol.673 , pp. 1-17
    • Nagarajan, N.1    Pop, M.2
  • 5
    • 84859178440 scopus 로고    scopus 로고
    • De novo genome assembly: What every biologist should know
    • Baker, M.: De novo genome assembly: what every biologist should know. Nature Methods 9, 333-337 (2012)
    • (2012) Nature Methods , vol.9 , pp. 333-337
    • Baker, M.1
  • 6
    • 70349212271 scopus 로고    scopus 로고
    • Parametric complexity of sequence assembly: Theory and applications to next generation sequencing
    • Nagarajan, N., Pop, M.: Parametric complexity of sequence assembly: theory and applications to next generation sequencing. Journal of Computational Biology 16(7), 897-908 (2009)
    • (2009) Journal of Computational Biology , vol.16 , Issue.7 , pp. 897-908
    • Nagarajan, N.1    Pop, M.2
  • 7
    • 80955159932 scopus 로고    scopus 로고
    • Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
    • Gao, S., Sung, W.K., Nagarajan, N.: Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology 18(11), 1681-1691 (2011)
    • (2011) Journal of Computational Biology , vol.18 , Issue.11 , pp. 1681-1691
    • Gao, S.1    Sung, W.K.2    Nagarajan, N.3
  • 9
    • 43349084767 scopus 로고    scopus 로고
    • Scaffolding and validation of bacterial genome assemblies using optical restriction maps
    • Nagarajan, N., Read, T.D., Pop, M.: Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 24(10), 1229-1235 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.10 , pp. 1229-1235
    • Nagarajan, N.1    Read, T.D.2    Pop, M.3
  • 11
    • 77950814686 scopus 로고    scopus 로고
    • Finishing genomes with limited resources: Lessons from an ensemble of microbial genomes
    • Nagarajan, N., Cook, C., Bonaventura, M.D., et al.: Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics 11(242) (2010)
    • (2010) BMC Genomics , vol.11 , pp. 242
    • Nagarajan, N.1    Cook, C.2    Bonaventura, M.D.3
  • 12
    • 77949511368 scopus 로고    scopus 로고
    • Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
    • Zerbino, D.R., McEwen, G.K., Marguiles, E.H., Birney, E.: Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE 4(12) (2009)
    • (2009) PLoS ONE , vol.4 , Issue.12
    • Zerbino, D.R.1    McEwen, G.K.2    Marguiles, E.H.3    Birney, E.4
  • 13
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R.H., Zhu, J., Ruan, W., et al.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20, 265-272 (2010)
    • (2010) Genome Research , vol.20 , pp. 265-272
    • Li, R.H.1    Zhu, J.2    Ruan, W.3
  • 14
    • 77950658346 scopus 로고    scopus 로고
    • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    • Tsai, I.J., Otto, T.D., Berriman, M.: Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology 11, R41 (2010)
    • (2010) Genome Biology , vol.11
    • Tsai, I.J.1    Otto, T.D.2    Berriman, M.3
  • 15
    • 0029197192 scopus 로고
    • Combinatorial algorithms for DNA sequence assembly
    • Kececioglu, J.D., Myers, E.W.: Combinatorial algorithms for DNA sequence assembly. Algorithmica 13, 7-51 (1993)
    • (1993) Algorithmica , vol.13 , pp. 7-51
    • Kececioglu, J.D.1    Myers, E.W.2
  • 17
    • 27544497879 scopus 로고    scopus 로고
    • The fragment assembly string graph
    • Myers, E.W.: The fragment assembly string graph. Bioinformatics 21(2), 79-85 (2005)
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 79-85
    • Myers, E.W.1
  • 18
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • doi:10.1101/gr.074492.107
    • Zerbino, D., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research (2008), doi:10.1101/gr.074492. 107
    • (2008) Genome Research
    • Zerbino, D.1    Birney, E.2
  • 19
    • 84861437658 scopus 로고
    • On approximating the longest path in a graph
    • Karger, D., Motwani, R., Ramkumar, G.D.S.: On approximating the longest path in a graph. Algorithmica 18, 421-432 (1993)
    • (1993) Algorithmica , vol.18 , pp. 421-432
    • Karger, D.1    Motwani, R.2    Ramkumar, G.D.S.3
  • 21
    • 0003415585 scopus 로고
    • Algorithms for Eulerian Trails, Eulerian Graphs and Related Topics
    • Fleischner, H.: Algorithms for Eulerian Trails, Eulerian Graphs and Related Topics. Annals of Discrete Mathematics, Part 1 2(50), X.1C13 (1991)
    • (1991) Annals of Discrete Mathematics , vol.2 , Issue.50 PART 1
    • Fleischner, H.1
  • 22
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford, C., Schatz, M.C., Pop, M.: Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11(21) (2010)
    • (2010) BMC Bioinformatics , vol.11 , Issue.21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 23
    • 54949137701 scopus 로고    scopus 로고
    • Metasim: A sequencing simulator for genomics and metagenomics
    • Richter, D.C., Ott, F., Schmid, R., Huson, D.H.: Metasim: a sequencing simulator for genomics and metagenomics. PloS One 3(10) (2008)
    • (2008) PloS One , vol.3 , Issue.10
    • Richter, D.C.1    Ott, F.2    Schmid, R.3    Huson, D.H.4
  • 24
    • 78649358717 scopus 로고    scopus 로고
    • Quake: Quality-aware detection and correction of sequencing errors
    • Kelley, D.R., Schatz, M.C., Salzberg, S.L.: Quake: quality-aware detection and correction of sequencing errors. Genome Biology 11, R116 (2010)
    • (2010) Genome Biology , vol.11
    • Kelley, D.R.1    Schatz, M.C.2    Salzberg, S.L.3
  • 25
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S.A., Phillippy, A., Delcher, A.L., et al.: Versatile and open software for comparing large genomes. Genome Biology 5, R12 (2004)
    • (2004) Genome Biology , vol.5
    • Kurtz, S.A.1    Phillippy, A.2    Delcher, A.L.3
  • 26
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14) (2002)
    • (2002) Nucleic Acids Research , vol.30 , Issue.14
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 27
    • 80051839847 scopus 로고    scopus 로고
    • Meraculous: De Novo Genome Assembly with Short Paired-End Reads
    • doi:10.1371/journal.pone.0023501
    • Jarrod, A.C., Isaac, H., Sirisha, S., Shujun, L., Gary, P.S., Daniel, S.R.: Meraculous: De Novo Genome Assembly with Short Paired-End Reads. PLoS ONE 6(8), e23501 (2011), doi:10.1371/journal.pone.0023501
    • (2011) PLoS ONE , vol.6 , Issue.8
    • Jarrod, A.C.1    Isaac, H.2    Sirisha, S.3    Shujun, L.4    Gary, P.S.5    Daniel, S.R.6
  • 28
    • 0030106462 scopus 로고    scopus 로고
    • Semidefinite Programming
    • Vandenberghe, L., Boyd, S.: Semidefinite Programming. SIAM Review 38, 49-95 (1996)
    • (1996) SIAM Review , vol.38 , pp. 49-95
    • Vandenberghe, L.1    Boyd, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.