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Volumn 7, Issue 2, 2012, Pages

CAPRG: Sequence assembling pipeline for next generation sequencing of non-model organisms

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; COLINUS; COLINUS VIRGINIANUS; CONTIG MAPPING; CONTROLLED STUDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; NONHUMAN; PHYLOGENY; PROTEIN ASSEMBLY; REFERENCE DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS; ALGORITHM; ANIMAL; BIOLOGY; BIRD; EVALUATION; GENE EXPRESSION PROFILING; GENOMICS; METHODOLOGY;

EID: 84856511197     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030370     Document Type: Article
Times cited : (4)

References (36)
  • 1
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 2
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next generation sequencing
    • Li H, Homer N, (2010) A survey of sequence alignment algorithms for next generation sequencing. Briefings in Bioinformatics 11 (5): 473-483.
    • (2010) Briefings in Bioinformatics , vol.11 , Issue.5 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 4
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang XQ, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Research 9: 868-877.
    • (1999) Genome Research , vol.9 , pp. 868-877
    • Huang, X.Q.1    Madan, A.2
  • 5
    • 0008068437 scopus 로고    scopus 로고
    • Phrap documentation
    • Green P, (1996) Phrap documentation. http://www.phrap.org/phredphrap/phrap.html.
    • (1996)
    • Green, P.1
  • 6
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
    • (2008) Genome Research , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 7
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller JR, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 8
    • 77957926979 scopus 로고    scopus 로고
    • Comparing de novo assemblers for 454 transcriptome data
    • Kumar S, Blaxter ML, (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11: 571.
    • (2010) BMC Genomics , vol.11 , pp. 571
    • Kumar, S.1    Blaxter, M.L.2
  • 9
    • 0037460985 scopus 로고    scopus 로고
    • TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    • Pertea G, Huang X, Liang F, Antonescu V, Sultana R, et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
    • (2003) Bioinformatics , vol.19 , pp. 651-652
    • Pertea, G.1    Huang, X.2    Liang, F.3    Antonescu, V.4    Sultana, R.5
  • 11
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research 14: 1147-1159.
    • (2004) Genome Research , vol.14 , pp. 1147-1159
    • Chevreux, B.1    Pfisterer, T.2    Drescher, B.3    Driesel, A.J.4    Müller, W.E.G.5
  • 12
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • Li RQ, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.Q.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 13
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • Li RQ, Yu C, Li Y, Lam T, Yiu S, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.Q.1    Yu, C.2    Li, Y.3    Lam, T.4    Yiu, S.5
  • 14
    • 77958453970 scopus 로고    scopus 로고
    • Reference-Free Validation of Short Read Data
    • Schroder J, Bailey J, Conway T, Zobel J, (2010) Reference-Free Validation of Short Read Data. Plos One 5 (9): e12681.
    • (2010) Plos One , vol.5 , Issue.9
    • Schroder, J.1    Bailey, J.2    Conway, T.3    Zobel, J.4
  • 15
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 16
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 17
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10 (3): R25.
    • (2009) Genome Biology , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 18
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler Transform
    • Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25: 1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 19
    • 84856517223 scopus 로고    scopus 로고
    • Novocraft aligner website
    • Available:. Accessed 2011, Aug 28
    • Novocraft aligner website. Available: http://www.novocraft.com. Accessed 2011, Aug 28.
  • 20
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • doi:10.1101/gr.111120.110
    • Lunter G, Goodson M, (2010) Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research doi:10.1101/gr.111120.110.
    • (2010) Genome Research
    • Lunter, G.1    Goodson, M.2
  • 22
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent WJ, (2002) BLAT- The BLAST-like alignment tool. Genome Research 12: 656-664.
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 23
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • Ning ZM, Cox AJ, Mullikin JC, (2001) SSAHA: A fast search method for large DNA databases. Genome Research 11: 1725-1729.
    • (2001) Genome Research , vol.11 , pp. 1725-1729
    • Ning, Z.M.1    Cox, A.J.2    Mullikin, J.C.3
  • 24
    • 60149098267 scopus 로고    scopus 로고
    • SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
    • Barker MS, Dlugosch KM, Reddy ACC, Amyotte SN, Rieseberg LH, (2009) SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses. Bioinformatics 25: 535-536.
    • (2009) Bioinformatics , vol.25 , pp. 535-536
    • Barker, M.S.1    Dlugosch, K.M.2    Reddy, A.C.C.3    Amyotte, S.N.4    Rieseberg, L.H.5
  • 28
    • 70350688130 scopus 로고    scopus 로고
    • Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
    • Dutilh BE, Huynen MA, Strous M, (2009) Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics 25: 2878-2881.
    • (2009) Bioinformatics , vol.25 , pp. 2878-2881
    • Dutilh, B.E.1    Huynen, M.A.2    Strous, M.3
  • 30
    • 77955464209 scopus 로고    scopus 로고
    • From raw materials to validated system: The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite
    • Rawat A, Gust KA, Deng Y, Garcia-Reyero N, Quinn MJ Jr, et al. (2010) From raw materials to validated system: The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. Physiological Genomics 42 (2): 219-35.
    • (2010) Physiological Genomics , vol.42 , Issue.2 , pp. 219-235
    • Rawat, A.1    Gust, K.A.2    Deng, Y.3    Garcia-Reyero, N.4    Quinn Jr., M.J.5
  • 31
    • 84856517135 scopus 로고    scopus 로고
    • Short Read Archive website
    • Available:. Accessed 2010, Feb 11
    • Short Read Archive website. Available: http://www.ncbi.nlm.nih.gov/Traces/sra. Accessed 2010, Feb 11.
  • 32
    • 84856517222 scopus 로고    scopus 로고
    • Seqclean website
    • Available. Accessed 2010, Jan 26
    • Seqclean website. Available http://compbio.dfci.harvard.edu/tgi/software. Accessed 2010, Jan 26.
  • 34
    • 84888287647 scopus 로고    scopus 로고
    • Entrez website
    • Available. Accessed 2010, Aug 10
    • Entrez website. Available http://www.ncbi.nlm.nih.gov/sites/gquery. Accessed 2010, Aug 10.
  • 35
    • 84856539268 scopus 로고    scopus 로고
    • Golden Path website
    • Available. Accessed 2010, Dec 2
    • Golden Path website. Available http://genome.ucsc.edu. Accessed 2010, Dec 2.
  • 36
    • 33746047855 scopus 로고    scopus 로고
    • The Design, Implementation, and Evaluation of mpiBLAST
    • 4th International Conference on Linux Clusters: The HPC Revolution 2003 in conjunction with ClusterWorld Conference & Expo
    • Darling A, Carey L, Feng W, (2003) The Design, Implementation, and Evaluation of mpiBLAST. 4th International Conference on Linux Clusters: The HPC Revolution 2003 in conjunction with ClusterWorld Conference & Expo.
    • (2003)
    • Darling, A.1    Carey, L.2    Feng, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.