메뉴 건너뛰기




Volumn 5, Issue FEB, 2014, Pages

A glance at quality score: Implication for de novo transcriptome reconstruction of Illumina reads

Author keywords

Oases; Quality score; RNA Seq; Transcriptome reconstruction; Trinity; Truncated transfrags

Indexed keywords

NUCLEOTIDE; RNA; TRANSCRIPTOME;

EID: 84897691240     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00017     Document Type: Note
Times cited : (34)

References (23)
  • 2
    • 79951526698 scopus 로고    scopus 로고
    • Succinct data structures for assembling large genomes
    • doi: 10.1093/bioinformatics/btq697
    • Conway, T. C., and Bromage, A. J. (2011). Succinct data structures for assembling large genomes. Bioinformatics 27, 479-486. doi: 10.1093/bioinformatics/btq697.
    • (2011) Bioinformatics , vol.27 , pp. 479-486
    • Conway, T.C.1    Bromage, A.J.2
  • 3
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
    • doi: 10.1186/1471-2105-11-485
    • Cox, M. P., Peterson, D. A., and Biggs, P. J. (2010). SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform. 11:485. doi: 10.1186/1471-2105-11-485.
    • (2010) BMC Bioinform. , vol.11 , pp. 485
    • Cox, M.P.1    Peterson, D.A.2    Biggs, P.J.3
  • 4
    • 78649449778 scopus 로고    scopus 로고
    • A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing
    • doi: 10.1016/j.ygeno.2010.07.010
    • Cui, P., Lin, Q., Ding, F., Xin, C., Gong, W., Zhang, L., et al. (2010). A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 96, 259-265. doi: 10.1016/j.ygeno.2010.07.010.
    • (2010) Genomics , vol.96 , pp. 259-265
    • Cui, P.1    Lin, Q.2    Ding, F.3    Xin, C.4    Gong, W.5    Zhang, L.6
  • 6
    • 84887224285 scopus 로고    scopus 로고
    • FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms
    • doi: 10.3390/biology1030895
    • Dodt, M., Roehr, J., Ahmed, R., and Dieterich, C. (2012). FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1, 895-905. doi: 10.3390/biology1030895.
    • (2012) Biology , vol.1 , pp. 895-905
    • Dodt, M.1    Roehr, J.2    Ahmed, R.3    Dieterich, C.4
  • 7
    • 84877801923 scopus 로고    scopus 로고
    • A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly
    • doi:10.1186/1471-2164-14-167
    • Francis, W. R., Christianson, L. M., Kiko, R., Powers, M. L., Shaner, N. C., and Haddock, S. H. D. (2013). A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics 14:167. doi:10.1186/1471-2164-14-167.
    • (2013) BMC Genomics , vol.14 , pp. 167
    • Francis, W.R.1    Christianson, L.M.2    Kiko, R.3    Powers, M.L.4    Shaner, N.C.5    Haddock, S.H.D.6
  • 8
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • doi: 10.1038/nmeth.1613
    • Garber, M., Grabherr, M. G., Guttman, M., and Trapnell, C. (2011). Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8, 469-477. doi: 10.1038/nmeth.1613.
    • (2011) Nat. Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 9
    • 79951828683 scopus 로고    scopus 로고
    • De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification
    • doi: 10.1093/dnares/dsq028
    • Garg, R., Patel, R. K., Tyagi, A. K., and Jain, M. (2011). De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18, 53-63. doi: 10.1093/dnares/dsq028.
    • (2011) DNA Res. , vol.18 , pp. 53-63
    • Garg, R.1    Patel, R.K.2    Tyagi, A.K.3    Jain, M.4
  • 10
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • doi: 10.1038/nbt.1883
    • Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652. doi: 10.1038/nbt.1883.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3    Levin, J.Z.4    Thompson, D.A.5    Amit, I.6
  • 12
    • 78649358717 scopus 로고    scopus 로고
    • Quake: quality-aware detection and correction of sequencing errors
    • doi: 10.1186/gb-2010-11-11-r116
    • Kelley, D. R., Schatz, M. C., and Salzberg, S. L. (2010). Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 11, R116. doi: 10.1186/gb-2010-11-11-r116.
    • (2010) Genome Biol. , vol.11
    • Kelley, D.R.1    Schatz, M.C.2    Salzberg, S.L.3
  • 13
    • 6344229798 scopus 로고    scopus 로고
    • Introns and splicing elements of five diverse fungi
    • doi: 10.1128/EC.3.5.1088-1100.2004
    • Kupfer, D. M., Drabenstot, S. D., Buchanan, K. L., Lai, H., Zhu, H., Dyer, D. W., et al. (2004). Introns and splicing elements of five diverse fungi. Eukaryot. Cell 3, 1088-1100. doi: 10.1128/EC.3.5.1088-1100.2004.
    • (2004) Eukaryot. Cell , vol.3 , pp. 1088-1100
    • Kupfer, D.M.1    Drabenstot, S.D.2    Buchanan, K.L.3    Lai, H.4    Zhu, H.5    Dyer, D.W.6
  • 15
    • 84885140594 scopus 로고    scopus 로고
    • Improving transcriptome assembly through error correction of high-throughput sequence reads
    • doi: 10.7717/peerj.113
    • MacManes, M. D., and Eisen, M. B. (2013). Improving transcriptome assembly through error correction of high-throughput sequence reads. Peer J. 1:e113. doi: 10.7717/peerj.113.
    • (2013) Peer J. , vol.1
    • MacManes, M.D.1    Eisen, M.B.2
  • 16
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • doi: 10.1038/nrg3068.
    • Martin, J. A., and Wang, Z., (2011). Next-generation transcriptome assembly. Nat. Rev. Genet. 12, 671-682. doi: 10.1038/nrg3068.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 17
    • 77957287342 scopus 로고    scopus 로고
    • De novo assembly of short sequence reads
    • doi: 10.1093/bib/bbq020
    • Paszkiewicz, K., and Studholme, D. J. (2010). De novo assembly of short sequence reads. Brief. Bioinform. 11, 457-472. doi: 10.1093/bib/bbq020.
    • (2010) Brief. Bioinform. , vol.11 , pp. 457-472
    • Paszkiewicz, K.1    Studholme, D.J.2
  • 18
    • 79957814500 scopus 로고    scopus 로고
    • Correcting errors in short reads by multiple alignments
    • doi: 10.1093/bioinformatics/btr170
    • Salmela, L., and Schröder, J. (2011). Correcting errors in short reads by multiple alignments. Bioinformatics 27, 1455-1461. doi: 10.1093/bioinformatics/btr170.
    • (2011) Bioinformatics , vol.27 , pp. 1455-1461
    • Salmela, L.1    Schröder, J.2
  • 19
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • doi: 10.1093/bioinformatics/bts094
    • Schulz, M. H., Zerbino, D. R., Vingron, M., and Birney, E. (2012). Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-1092. doi: 10.1093/bioinformatics/bts094.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 20
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • doi:10.1186/1471-2105-6-31
    • Slater, G. S., and Birney, E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 6:31. doi:10.1186/1471-2105-6-31.
    • (2005) BMC Bioinform. , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 21
    • 80054784996 scopus 로고    scopus 로고
    • ConDeTri-a content dependent read trimmer for llumina data
    • doi: 10.1371/journal.pone.0026314
    • Smeds, L., and Künstner, A. (2011). ConDeTri-a content dependent read trimmer for llumina data. PLoS ONE 6:e26314. doi: 10.1371/journal.pone.0026314.
    • (2011) PLoS ONE , vol.6
    • Smeds, L.1    Künstner, A.2
  • 22
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    • doi: 10.1093/bioinformatics/bti310
    • Wu, T. D., and Watanabe, C. K. (2005). GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875. doi: 10.1093/bioinformatics/bti310.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 23
    • 77957758142 scopus 로고    scopus 로고
    • Reptile: representative tiling for short read error correction
    • doi: 10.1093/bioinformatics/btq468
    • Yang, X., Dorman, K. S., and Aluru, S. (2010). Reptile: representative tiling for short read error correction. Bioinformatics 26, 2526-2533. doi: 10.1093/bioinformatics/btq468.
    • (2010) Bioinformatics , vol.26 , pp. 2526-2533
    • Yang, X.1    Dorman, K.S.2    Aluru, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.