메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

Author keywords

[No Author keywords available]

Indexed keywords

COMMODITY HARDWARE; COMPUTATION TIME; EXON SKIPPING; FUSION GENES; GENE FUSION; HUMAN BREAST CANCER; LARGE DATASETS; MEMORY FOOTPRINT; MEMORY RESOURCES; MICRO ASSEMBLY; NEXT-GENERATION SEQUENCING; REGION OF INTEREST; REGIONS OF INTEREST; RESEARCH TOPICS; SHORT SEQUENCES; SPECIFIC INFORMATION; STRUCTURAL EVENTS;

EID: 84858730803     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-48     Document Type: Article
Times cited : (33)

References (19)
  • 1
    • 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, et al. 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
  • 2
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Meth 2011, 8:61-65. [http://dx.doi.org/10.1038/nmeth.1527], [http://www.nature.com/nmeth/journal/v8/n1/abs/nmeth.1527.html{set minus}#supplementary-information].
    • (2011) Nat Meth , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 3
    • 79960411408 scopus 로고    scopus 로고
    • Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies
    • Lin Y, Li J, Shen H, Zhang L, Papasian CJ, Deng HW. Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies. Bioinformatics (Oxford, England) 2011, 27(15):2031-2037. [http://www.ncbi.nlm.nih.gov/pubmed/21636596].
    • (2011) Bioinformatics (Oxford, England) , vol.27 , Issue.15 , pp. 2031-2037
    • Lin, Y.1    Li, J.2    Shen, H.3    Zhang, L.4    Papasian, C.J.5    Deng, H.W.6
  • 5
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • 10.1038/nprot.2007.324, 17947979
    • Cline MS, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2(10):2366-2382. [http://dx.doi.org/10.1038/nprot.2007.324], 10.1038/nprot.2007.324, 17947979.
    • (2007) Nat Protoc , vol.2 , Issue.10 , pp. 2366-2382
    • Cline, M.S.1
  • 7
    • 77957815609 scopus 로고    scopus 로고
    • GASSST: Global Alignment Short Sequence Search Tool
    • Rizk G, Lavenier D. GASSST: Global Alignment Short Sequence Search Tool. Bioinformatics (Oxford, England) 2010, 26(20):2534-2540. [http://www.ncbi.nlm.nih.gov/pubmed/20739310].
    • (2010) Bioinformatics (Oxford, England) , vol.26 , Issue.20 , pp. 2534-2540
    • Rizk, G.1    Lavenier, D.2
  • 8
    • 33847307402 scopus 로고    scopus 로고
    • Assembling millions of short DNA sequences using SSAKE
    • 10.1093/bioinformatics/btl629, 17158514
    • Warren RL, Sutton GG, Jones SJM, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 2007, 23(4):500-501. [http://dx.doi.org/10.1093/bioinformatics/btl629], 10.1093/bioinformatics/btl629, 17158514.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 500-501
    • Warren, R.L.1    Sutton, G.G.2    Jones, S.J.M.3    Holt, R.A.4
  • 9
    • 1842717960 scopus 로고    scopus 로고
    • The atlas genome assembly system
    • 10.1101/gr.2264004, 383319, 15060016
    • Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song X, Weinstock GM, Gibbs RA. The atlas genome assembly system. Genome Res 2004, 14(4):721-732. [http://genome.cshlp.org/content/14/4/721.abstract], 10.1101/gr.2264004, 383319, 15060016.
    • (2004) Genome Res , vol.14 , Issue.4 , pp. 721-732
    • Havlak, P.1    Chen, R.2    Durbin, K.J.3    Egan, A.4    Ren, Y.5    Song, X.6    Weinstock, G.M.7    Gibbs, R.A.8
  • 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. [http://dx.doi.org/10.1371], 10.1371/journal.pone.0019816, 3092772, 21589938.
    • (2011) PLoS ONE , vol.6 , Issue.5
    • Warren, R.L.1    Holt, R.A.2
  • 11
    • 77950658346 scopus 로고    scopus 로고
    • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    • 10.1186/gb-2010-11-4-r41, 2884544, 20388197
    • Tsai I, Otto T, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol 2010, 11(4):R41. [http://genomebiology.com/2010/11/4/R41], 10.1186/gb-2010-11-4-r41, 2884544, 20388197.
    • (2010) Genome Biol , vol.11 , Issue.4
    • Tsai, I.1    Otto, T.2    Berriman, M.3
  • 12
    • 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, Li S, Yang H, Wang J, Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20(2):265-272. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2813482{set minus}&tool=pmcentrez{set minus}&rendertype=abstract], 10.1101/gr.097261.109, 2813482, 20019144.
    • (2010) Genome Res , vol.20 , Issue.2 , pp. 265-272
    • 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    Li, S.11    Yang, H.12    Wang, J.13    Wang, J.14
  • 14
    • 0036250811 scopus 로고    scopus 로고
    • Alu repeats and human genomic diversity
    • 10.1038/nrg798, 11988762
    • Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002, 3(5):370-379. 10.1038/nrg798, 11988762.
    • (2002) Nat Rev Genet , vol.3 , Issue.5 , pp. 370-379
    • Batzer, M.A.1    Deininger, P.L.2
  • 16
  • 17
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-Like Alignment Tool
    • 187518, 11932250
    • Kent WJ. BLAT-The BLAST-Like Alignment Tool. Genome Res 2002, 12(4):656-664. [http://www.genome.org/cgi/doi/10.1101/gr.229202], 187518, 11932250.
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.