메뉴 건너뛰기




Volumn 8, Issue 1, 2013, Pages

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

Author keywords

Bloom filter; De Bruijn graph; De novo assembly

Indexed keywords

MEASLES VIRUS;

EID: 84883784774     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-8-22     Document Type: Article
Times cited : (247)

References (23)
  • 1
    • 0029312687 scopus 로고
    • A new algorithm for DNA sequence assembly
    • 10.1089/cmb.1995.2.291, 7497130
    • Idury RM, Waterman MS. A new algorithm for DNA sequence assembly. J Comput Biol 1995, 2(2):291-306. 10.1089/cmb.1995.2.291, 7497130.
    • (1995) J Comput Biol , vol.2 , Issue.2 , pp. 291-306
    • Idury, R.M.1    Waterman, M.S.2
  • 2
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 2011, 29(7):644-652. [http://dx.doi.org/10.1038/nbt.1883].
    • (2011) Nat Biotech , vol.29 , Issue.7 , pp. 644-652
    • Grabherr, M.G.1
  • 3
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: a de Novo assembler for metagenomic data
    • 10.1093/bioinformatics/btr216, 3117360, 21685107
    • Peng Y, Leung HCM, Yiu SM, Chin FYL. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 2011, 27(13):i94-i101. 10.1093/bioinformatics/btr216, 3117360, 21685107.
    • (2011) Bioinformatics , vol.27 , Issue.13
    • Peng, Y.1    Leung, H.C.M.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 5
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de Bruijn graphs
    • 10.1038/ng.1028, 3272472, 22231483
    • Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 2012, 44:226-232. 10.1038/ng.1028, 3272472, 22231483.
    • (2012) Nat Genet , vol.44 , pp. 226-232
    • Iqbal, Z.1    Caccamo, M.2    Turner, I.3    Flicek, P.4    McVean, G.5
  • 7
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • 10.1101/gr.097261.109, 2813482, 20019144
    • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20(2):265. 10.1101/gr.097261.109, 2813482, 20019144.
    • (2010) Genome Res , vol.20 , Issue.2 , pp. 265
    • Li, R.1    Zhu, H.2    Ruan, J.3    Qian, W.4    Fang, X.5    Shi, Z.6    Li, Y.7    Li, S.8    Shan, G.9    Kristiansen, K.10
  • 8
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • 10.1101/gr.089532.108, 2694472, 19251739
    • Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Res 2009, 19(6):1117-1123. [http://genome.cshlp.org/content/19/6/1117.abstract], 10.1101/gr.089532.108, 2694472, 19251739.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1117-1123
    • Simpson, J.T.1    Wong, K.2    Jackman, S.D.3    Schein, J.E.4    Jones, S.J.M.5    Birol, I.6
  • 9
    • 79951526698 scopus 로고    scopus 로고
    • Succinct data structures for assembling large genomes
    • 10.1093/bioinformatics/btq697, 21245053
    • Conway TC, Bromage AJ. Succinct data structures for assembling large genomes. Bioinformatics 2011, 27(4):479. 10.1093/bioinformatics/btq697, 21245053.
    • (2011) Bioinformatics , vol.27 , Issue.4 , pp. 479
    • Conway, T.C.1    Bromage, A.J.2
  • 10
    • 79955919332 scopus 로고    scopus 로고
    • Targeted assembly of short sequence reads
    • 10.1371/journal.pone.0019816, 3092772, 21589938
    • Warren RL, Holt RA. Targeted assembly of short sequence reads. PloS One 2011, 6(5):e19816. 10.1371/journal.pone.0019816, 3092772, 21589938.
    • (2011) PloS One , vol.6 , Issue.5
    • Warren, R.L.1    Holt, R.A.2
  • 11
    • 84858730803 scopus 로고    scopus 로고
    • Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer
    • 10.1186/1471-2105-13-48, 3514201, 22443449
    • Peterlongo P, Chikhi R. Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinformatics 2012, 13:48. 10.1186/1471-2105-13-48, 3514201, 22443449.
    • (2012) BMC Bioinformatics , vol.13 , pp. 48
    • Peterlongo, P.1    Chikhi, R.2
  • 12
    • 84866712746 scopus 로고    scopus 로고
    • Exploiting sparseness in de novo genome assembly
    • 10.1186/1471-2105-13-S6-S1, 23346590
    • Ye C, Ma Z, Cannon C, Pop M, Yu D. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics 2012, 13(Suppl 6):S1. [http://www.biomedcentral.com/1471-2105/13/S6/S1], 10.1186/1471-2105-13-S6-S1, 23346590.
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL 6
    • Ye, C.1    Ma, Z.2    Cannon, C.3    Pop, M.4    Yu, D.5
  • 14
    • 33750722107 scopus 로고    scopus 로고
    • Less hashing, same performance: Building a better Bloom filter
    • Kirsch A, Mitzenmacher M. Less hashing, same performance: Building a better Bloom filter. Algorithms-ESA 2006, 4168:456-467.
    • (2006) Algorithms-ESA , vol.4168 , pp. 456-467
    • Kirsch, A.1    Mitzenmacher, M.2
  • 15
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • 10.1016/j.ygeno.2010.03.001, 2874646, 20211242
    • Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95(6):315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
    • (2010) Genomics , vol.95 , Issue.6 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 16
    • 80052983218 scopus 로고    scopus 로고
    • Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph
    • Chikhi R, Lavenier D. Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph. Algo Bioinformatics 2011, 6833:39-48.
    • (2011) Algo Bioinformatics , vol.6833 , pp. 39-48
    • Chikhi, R.1    Lavenier, D.2
  • 17
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • 10.1186/1471-2105-11-21, 2821320, 20064276
    • Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 2010, 11:21. 10.1186/1471-2105-11-21, 2821320, 20064276.
    • (2010) BMC Bioinformatics , vol.11 , pp. 21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 18
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • 10.1093/bioinformatics/btr011, 3051319, 21217122
    • Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27(6):764-770. [http://bioinformatics.oxfordjournals.org/content/27/6/764.abstract], 10.1093/bioinformatics/btr011, 3051319, 21217122.
    • (2011) Bioinformatics , vol.27 , Issue.6 , pp. 764-770
    • Marçais, G.1    Kingsford, C.2
  • 19
    • 84874741072 scopus 로고    scopus 로고
    • DSK: k-mer counting with very low memory usage
    • 10.1093/bioinformatics/btt020, 23325618
    • Rizk G, Lavenier D, Chikhi R. DSK: k-mer counting with very low memory usage. Bioinformatics 2013, 29(5):652-653. 10.1093/bioinformatics/btt020, 23325618.
    • (2013) Bioinformatics , vol.29 , Issue.5 , pp. 652-653
    • Rizk, G.1    Lavenier, D.2    Chikhi, R.3
  • 20
    • 77957815609 scopus 로고    scopus 로고
    • GASSST: global alignment short sequence search tool
    • 10.1093/bioinformatics/btq485, 2951093, 20739310
    • Rizk G, Lavenier D. GASSST: global alignment short sequence search tool. Bioinformatics 2010, 26(20):2534. 10.1093/bioinformatics/btq485, 2951093, 20739310.
    • (2010) Bioinformatics , vol.26 , Issue.20 , pp. 2534
    • Rizk, G.1    Lavenier, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.