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Volumn 6, Issue 6, 2015, Pages 725-734

Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

Author keywords

Ancient DNA; Bioinformatics; Genomes; Laboratory methods; Molecular biology; Sequence data

Indexed keywords


EID: 84931575449     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12353     Document Type: Article
Times cited : (38)

References (31)
  • 3
    • 84902346093 scopus 로고    scopus 로고
    • Library construction for ancient genomics: single strand or double strand?
    • 292-296, 298.
    • Bennett, E.A., Massilani, D., Lizzo, G., Daligault, J., Geigl, E.-M. & Grange, T. (2014). Library construction for ancient genomics: single strand or double strand? BioTechniques, 56, 289-290, 292-296, 298.
    • (2014) BioTechniques , vol.56 , pp. 289-290
    • Bennett, E.A.1    Massilani, D.2    Lizzo, G.3    Daligault, J.4    Geigl, E.-M.5    Grange, T.6
  • 5
    • 67650831473 scopus 로고    scopus 로고
    • Targeted retrieval and analysis of five Neandertal mtDNA genomes
    • Briggs, A.W., Good, J.M., Green, R.E., Krause, J., Maricic, T., Stenzel, U. et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 325, 318-321.
    • (2009) Science , vol.325 , pp. 318-321
    • Briggs, A.W.1    Good, J.M.2    Green, R.E.3    Krause, J.4    Maricic, T.5    Stenzel, U.6
  • 6
    • 77952206860 scopus 로고    scopus 로고
    • Targeted investigation of the Neandertal genome by array-based sequence capture
    • Burbano, H.A., Hodges, E., Green, R.E., Briggs, A.W., Krause, J., Meyer, M. et al. (2010) Targeted investigation of the Neandertal genome by array-based sequence capture. Science, 328, 723-725.
    • (2010) Science , vol.328 , pp. 723-725
    • Burbano, H.A.1    Hodges, E.2    Green, R.E.3    Briggs, A.W.4    Krause, J.5    Meyer, M.6
  • 8
    • 0036781906 scopus 로고    scopus 로고
    • Comparative analysis of comparative genomic hybridization microarray technologies: report of a workshop sponsored by the Wellcome Trust
    • Carter, N.P., Fiegler, H. & Piper, J. (2002) Comparative analysis of comparative genomic hybridization microarray technologies: report of a workshop sponsored by the Wellcome Trust. Cytometry, 49, 43-48.
    • (2002) Cytometry , vol.49 , pp. 43-48
    • Carter, N.P.1    Fiegler, H.2    Piper, J.3
  • 10
    • 84875700725 scopus 로고    scopus 로고
    • Predicting the molecular complexity of sequencing libraries
    • Daley, T. & Smith, A.D. (2013) Predicting the molecular complexity of sequencing libraries. Nature Methods, 10, 325-327.
    • (2013) Nature Methods , vol.10 , pp. 325-327
    • Daley, T.1    Smith, A.D.2
  • 13
    • 84876151646 scopus 로고    scopus 로고
    • A revised timescale for human evolution based on ancient mitochondrial genomes
    • Fu, Q., Mittnik, A., Johnson, P.L.F., Bos, K., Lari, M., Bollongino, R. et al. (2013b) A revised timescale for human evolution based on ancient mitochondrial genomes. Current Biology, 23, 553-559.
    • (2013) Current Biology , vol.23 , pp. 553-559
    • Fu, Q.1    Mittnik, A.2    Johnson, P.L.F.3    Bos, K.4    Lari, M.5    Bollongino, R.6
  • 14
    • 84875500588 scopus 로고    scopus 로고
    • Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA
    • Gansauge, M.T. & Meyer, M. (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols, 8, 737-748.
    • (2013) Nature Protocols , vol.8 , pp. 737-748
    • Gansauge, M.T.1    Meyer, M.2
  • 15
    • 84972492387 scopus 로고
    • Inference from iterative simulation using multiple sequences
    • Gelman, A. & Rubin, D.B. (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457-472.
    • (1992) Statistical Science , vol.7 , pp. 457-472
    • Gelman, A.1    Rubin, D.B.2
  • 16
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W. et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology, 27, 182-189.
    • (2009) Nature Biotechnology , vol.27 , pp. 182-189
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3    Rogov, P.4    LeProust, E.M.5    Brockman, W.6
  • 17
    • 84879910635 scopus 로고    scopus 로고
    • mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
    • Jonsson, H., Ginolhac, A., Schubert, M., Johnson, P.L. & Orlando, L. (2013) mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics, 29, 1682-1684.
    • (2013) Bioinformatics , vol.29 , pp. 1682-1684
    • Jonsson, H.1    Ginolhac, A.2    Schubert, M.3    Johnson, P.L.4    Orlando, L.5
  • 18
    • 79952098463 scopus 로고    scopus 로고
    • Next generation sequencing of ancient DNA: requirements, strategies and perspectives
    • Knapp, M. & Hofreiter, M. (2010) Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes, 1, 227-243.
    • (2010) Genes , vol.1 , pp. 227-243
    • Knapp, M.1    Hofreiter, M.2
  • 19
    • 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, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 21
    • 84863101693 scopus 로고    scopus 로고
    • AdapterRemoval: easy cleaning of next generation sequencing reads
    • Lindgreen, S. (2012) AdapterRemoval: easy cleaning of next generation sequencing reads. BMC Research Notes, 5, 337.
    • (2012) BMC Research Notes , vol.5 , pp. 337
    • Lindgreen, S.1
  • 22
    • 78649512174 scopus 로고    scopus 로고
    • Multiplexed DNA sequence capture of mitochondrial genomes using PCR products
    • Maricic, T., Whitten, M. & Paabo, S. (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE, 5, e14004.
    • (2010) PLoS ONE , vol.5 , pp. e14004
    • Maricic, T.1    Whitten, M.2    Paabo, S.3
  • 23
    • 77956285690 scopus 로고    scopus 로고
    • Illumina sequencing library preparation for highly multiplexed target capture and sequencing
    • 2010, pdb prot5448.
    • Meyer, M. & Kircher, M. (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols, 2010, pdb prot5448.
    • (2010) Cold Spring Harbor Protocols
    • Meyer, M.1    Kircher, M.2
  • 24
    • 84867331947 scopus 로고    scopus 로고
    • A high-coverage genome sequence from an archaic Denisovan individual
    • Meyer, M., Kircher, M., Gansauge, M.T., Li, H., Racimo, F., Mallick, S. et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222-226.
    • (2012) Science , vol.338 , pp. 222-226
    • Meyer, M.1    Kircher, M.2    Gansauge, M.T.3    Li, H.4    Racimo, F.5    Mallick, S.6
  • 25
    • 31144444397 scopus 로고    scopus 로고
    • Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect
    • Newkirk, H.L., Knoll, J.H. & Rogan, P.K. (2005) Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect. Nucleic Acids Research, 33, e191.
    • (2005) Nucleic Acids Research , vol.33 , pp. e191
    • Newkirk, H.L.1    Knoll, J.H.2    Rogan, P.K.3
  • 26
    • 41149087694 scopus 로고    scopus 로고
    • CODA: convergence diagnosis and output analysis for MCMC
    • Plummer, M., Best, N., Cowles, K. & Vines, K. (2006) CODA: convergence diagnosis and output analysis for MCMC. R News, 6, 7-11.
    • (2006) R News , vol.6 , pp. 7-11
    • Plummer, M.1    Best, N.2    Cowles, K.3    Vines, K.4
  • 27
    • 84893961036 scopus 로고    scopus 로고
    • The genome of a Late Pleistocene human from a Clovis burial site in western Montana
    • Rasmussen, M., Anzick, S.L., Waters, M.R., Skoglund, P., DeGiorgio, M., Stafford, T.W. Jr et al. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature, 506, 225-229.
    • (2014) Nature , vol.506 , pp. 225-229
    • Rasmussen, M.1    Anzick, S.L.2    Waters, M.R.3    Skoglund, P.4    DeGiorgio, M.5    Stafford Jr, T.W.6
  • 28
    • 34548579114 scopus 로고    scopus 로고
    • Ancient DNA extraction from bones and teeth
    • Rohland, N. & Hofreiter, M. (2007) Ancient DNA extraction from bones and teeth. Nature Protocols, 2, 1756-1762.
    • (2007) Nature Protocols , vol.2 , pp. 1756-1762
    • Rohland, N.1    Hofreiter, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.