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Volumn 29, Issue 8, 2013, Pages 1004-1010

EBARDenovo: Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84876266164     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt092     Document Type: Article
Times cited : (28)

References (24)
  • 1
    • 77953553548 scopus 로고    scopus 로고
    • Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    • Agarwal, A. et al. (2010) Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics, 11, 383.
    • (2010) BMC Genomics , vol.11 , pp. 383
    • Agarwal, A.1
  • 2
    • 84870815979 scopus 로고    scopus 로고
    • Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript
    • Benelli, M. et al. (2012) Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript. Bioinformatics, 28, 3232-3239.
    • (2012) Bioinformatics , vol.28 , pp. 3232-3239
    • Benelli, M.1
  • 4
    • 0032703998 scopus 로고    scopus 로고
    • D2-cluster: A validated method for clustering EST and full-length cDNAsequences
    • Burke, J. et al. (1999) d2-cluster: a validated method for clustering EST and full-length cDNAsequences. Genome Res., 9, 1135-1142.
    • (1999) Genome Res. , vol.9 , pp. 1135-1142
    • Burke, J.1
  • 5
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: de novo assembly of whole-genome shotgun microreads
    • Butler, J. et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1
  • 6
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera de- tection
    • Edgar, R.C. et al. (2011) UCHIME improves sensitivity and speed of chimera de- tection. Bioinformatics, 2194-2200.
    • (2011) Bioinformatics , pp. 2194-2200
    • Edgar, R.C.1
  • 7
    • 84866041346 scopus 로고    scopus 로고
    • RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis
    • Garcia, T.I. et al. (2012) RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis. BMC Genomics, 13, 474.
    • (2012) BMC Genomics , vol.13 , pp. 474
    • Garcia, T.I.1
  • 8
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 9
    • 80054003528 scopus 로고    scopus 로고
    • ChimeraScan: A tool for identifying chimeric transcription in sequencing data
    • Iyer, M.K. et al. (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics, 2093-2094.
    • (2011) Bioinformatics , pp. 2093-2094
    • Iyer, M.K.1
  • 10
    • 80052521697 scopus 로고    scopus 로고
    • Synthetic spike-in standards for RNA-seq experiments
    • Jiang, L. et al. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Res., 21, 1543-1551.
    • (2011) Genome Res. , vol.21 , pp. 1543-1551
    • Jiang, L.1
  • 11
    • 12144287461 scopus 로고    scopus 로고
    • Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    • Kampa, D. et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res., 14, 331-342.
    • (2004) Genome Res. , vol.14 , pp. 331-342
    • Kampa, D.1
  • 12
    • 79960852002 scopus 로고    scopus 로고
    • Addressing challenges in the production and analysis of illumina sequencing data
    • Kircher, M. et al. (2011) Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12, 382-395.
    • (2011) BMC Genomics , vol.12 , pp. 382-395
    • Kircher, M.1
  • 13
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1
  • 14
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1
  • 15
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner, P. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-9753.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9748-9753
    • Pevzner, P.1
  • 16
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Pruitt, K.D. et al. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
    • (2012) Nucleic Acids Res. , vol.40
    • Pruitt, K.D.1
  • 17
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • Rhee, S.Y. et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res., 31, 224-228.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 224-228
    • Rhee, S.Y.1
  • 18
    • 78049346632 scopus 로고    scopus 로고
    • De novo assembly and analysis of RNA-seq data
    • Robertson, G. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909-912.
    • (2010) Nat. Methods , vol.7 , pp. 909-912
    • Robertson, G.1
  • 19
    • 84859768479 scopus 로고    scopus 로고
    • Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz, M.H. et al. (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28, 1086-1092.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1
  • 20
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • Shiraki, T. et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA, 100, 15776-15781.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 15776-15781
    • Shiraki, T.1
  • 21
    • 0042835830 scopus 로고    scopus 로고
    • Chromosomal translocations involved in non-Hodgkin lymphomas
    • Vega, F. and Medeiros, LJ. (2003) Chromosomal translocations involved in non-Hodgkin lymphomas. Arch. Pathol. Lab. Med., 127, 1148-1160.
    • (2003) Arch. Pathol. Lab. Med. , vol.127 , pp. 1148-1160
    • Vega, F.1    Medeiros, L.J.2
  • 22
    • 0028789793 scopus 로고
    • Serial analysis of gene expression
    • Velculescu, V.E. et al. (1995) Serial analysis of gene expression. Science, 270, 484-487.
    • (1995) Science , vol.270 , pp. 484-487
    • Velculescu, V.E.1
  • 23
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: A genomic mapping and alignment program for mRNA and EST sequences
    • Wu, T.D. and Watanabe, C.K. (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 24
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.1    Birney, E.2


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