메뉴 건너뛰기




Volumn 5, Issue , 2015, Pages

Illumina synthetic long read sequencing allows recovery of missing sequences even in the "Finished" C. elegans genome

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CAENORHABDITIS ELEGANS; GENETIC VARIATION; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; REPRODUCIBILITY;

EID: 84930667103     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10814     Document Type: Article
Times cited : (52)

References (29)
  • 1
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan, C., Sajjadian, S. & Eichler, E. E. Limitations of next-generation genome sequence assembly. Nature methods 8, 61-65, doi: 10.1038/nmeth.1527 (2011
    • (2011) Nature Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 2
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59, doi: 10.1038/nature07517 (2008
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 3
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1
  • 4
    • 84863664355 scopus 로고    scopus 로고
    • A hybrid approach for the automated finishing of bacterial genomes
    • Bashir, A. et al. A hybrid approach for the automated finishing of bacterial genomes. Nature biotechnology 30, 701-707 (2012
    • (2012) Nature Biotechnology , vol.30 , pp. 701-707
    • Bashir, A.1
  • 5
    • 84864518203 scopus 로고    scopus 로고
    • Pacific biosciences sequencing technology for genotyping and variation discovery in human data
    • Carneiro, M. O. et al. Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC genomics 13, 375, doi: 10.1186/1471-2164-13-375 (2012
    • (2012) BMC Genomics , vol.13 , pp. 375
    • Carneiro, M.O.1
  • 6
    • 84881496498 scopus 로고    scopus 로고
    • The genome sequence of the colonial chordate Botryllus schlosseri
    • Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. eLife 2, e00569, doi: 10.7554/ eLife.00569 (2013
    • (2013) ELife , vol.2 , pp. e00569
    • Voskoboynik, A.1
  • 7
    • 84898654757 scopus 로고    scopus 로고
    • Whole-genome haplotyping using long reads and statistical methods
    • Kuleshov, V. et al. Whole-genome haplotyping using long reads and statistical methods. Nature biotechnology 32, 261-266, doi: Doi 10.1038/Nbt.2833 (2014
    • Nature Biotechnology , vol.32 , pp. 261-266
    • Kuleshov, V.1
  • 8
    • 84907087679 scopus 로고    scopus 로고
    • Illumina TruSeq Synthetic Long-Reads Empower de Novo Assembly and Resolve Complex
    • McCoy, R. C. et al. Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements. PLoS One 9, e106689, doi: 10.1371/journal.pone.0106689 (2014
    • (2014) Highly-Repetitive Transposable Elements. PLoS One , vol.9 , pp. e106689
    • McCoy, R.C.1
  • 9
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C elegans: A platform for investigating biology
    • New York, N.Y.
    • Consortium, C. e. S. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science (New York, N.Y.) 282, 2012-2018 (1998
    • (1998) Science , vol.282 , pp. 2012-2018
    • Consortium, C.E.S.1
  • 10
    • 38749149152 scopus 로고    scopus 로고
    • Whole-genome sequencing and variant discovery in C elegans
    • Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nature methods 5, 183-188, doi: 10.1038/ nmeth.1179 (2008
    • (2008) Nature Methods , vol.5 , pp. 183-188
    • Hillier, L.W.1
  • 11
    • 80051688000 scopus 로고    scopus 로고
    • Field guide to next-generation DNA sequencers
    • Glenn, T. C. Field guide to next-generation DNA sequencers. Molecular ecology resources 11, 759-769, doi: 10.1111/j.1755-0998.2011.03024.x (2011
    • (2011) Molecular Ecology Resources , vol.11 , pp. 759-769
    • Glenn, T.C.1
  • 12
    • 0022649450 scopus 로고
    • The rDNA of C. Elegans: Sequence and structure
    • Ellis, R., Sulston, J. & Coulson, A. The rDNA of C. elegans: sequence and structure. Nucleic acids research 14, 2345-2364 (1986
    • (1986) Nucleic Acids Research , vol.14 , pp. 2345-2364
    • Ellis, R.1    Sulston, J.2    Coulson, A.3
  • 13
    • 0022397022 scopus 로고
    • Genes coding for 5S ribosomal RNA of the nematode Caenorhabditis elegans
    • Nelson, D. W. & Honda, B. M. Genes coding for 5S ribosomal RNA of the nematode Caenorhabditis elegans. Gene 38, 245-251 (1985
    • (1985) Gene , vol.38 , pp. 245-251
    • Nelson, D.W.1    Honda, B.M.2
  • 14
    • 0346494826 scopus 로고    scopus 로고
    • WormBase: A multi-species resource for nematode biology and genomics
    • Harris, T. W. et al. WormBase: a multi-species resource for nematode biology and genomics. Nucleic acids research 32, D411-D417 (2004
    • (2004) Nucleic Acids Research , vol.32 , pp. D411-D417
    • Harris, T.W.1
  • 16
    • 75549084124 scopus 로고    scopus 로고
    • WormBase: A comprehensive resource for nematode research
    • Harris, T. W. et al. WormBase: a comprehensive resource for nematode research. Nucleic acids research, gkp952 (2009
    • (2009) Nucleic Acids Research gkp952
    • Harris, T.W.1
  • 17
    • 78649740727 scopus 로고    scopus 로고
    • Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. Elegans
    • e13922
    • Weber, K. P. et al. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One 5, e13922, doi: 10.1371/journal.pone.0013922 (2010
    • (2010) PLoS One , vol.5
    • Weber, K.P.1
  • 19
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods 10, 563-569, doi: 10.1038/nmeth.2474 (2013
    • (2013) Nature Methods , vol.10 , pp. 563-569
    • Chin, C.S.1
  • 20
    • 61849109937 scopus 로고    scopus 로고
    • Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
    • Barri?e, A. et al. Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome research 19, 470-480 (2009
    • (2009) Genome Research , vol.19 , pp. 470-480
    • Barrie, A.1
  • 21
    • 84924370275 scopus 로고    scopus 로고
    • A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. Nigoni
    • Bi, Y. et al. A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni. PLoS genetics 11, e1004993-e1004993 (2015
    • (2015) PLoS Genetics , vol.11 , pp. e1004993-e1004993
    • Bi, Y.1
  • 22
    • 84865654186 scopus 로고    scopus 로고
    • A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species
    • Yan, C., Bi, Y., Yin, D. & Zhao, Z. A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species. PloS one 7, e43770 (2012
    • (2012) PloS One , vol.7 , pp. e43770
    • Yan, C.1    Bi, Y.2    Yin, D.3    Zhao, Z.4
  • 23
    • 84863651532 scopus 로고    scopus 로고
    • Hybrid error correction and de novo assembly of single-molecule sequencing reads
    • Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature biotechnology 30, 693-700 (2012
    • (2012) Nature Biotechnology , vol.30 , pp. 693-700
    • Koren, S.1
  • 24
    • 77949587649 scopus 로고    scopus 로고
    • And accurate long-read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595, doi: 10.1093/bioinformatics/btp698 (2010
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Fast, D.R.2
  • 25
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 26
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 28
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J. C. et al. The sequence of the human genome. Science (New York, N.Y.) 291, 1304-1351 (2001
    • (2001) Science (New York, N.Y.) , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 29
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075 (2013
    • (2013) Bioinformatics , vol.29 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.