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Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination

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Abstract
Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.
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GENOMES

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MLA
Van Nieuwerburgh, Filip, Ryan C Thompson, Jessica Ledesma, et al. “Illumina Mate-paired DNA Sequencing-library Preparation Using Cre-Lox Recombination.” NUCLEIC ACIDS RESEARCH 40.3 (2012): n. pag. Print.
APA
Van Nieuwerburgh, Filip, Thompson, R. C., Ledesma, J., Deforce, D., Gaasterland, T., Ordoukhanian, P., & Head, S. R. (2012). Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. NUCLEIC ACIDS RESEARCH, 40(3).
Chicago author-date
Van Nieuwerburgh, Filip, Ryan C Thompson, Jessica Ledesma, Dieter Deforce, Terry Gaasterland, Phillip Ordoukhanian, and Steven R Head. 2012. “Illumina Mate-paired DNA Sequencing-library Preparation Using Cre-Lox Recombination.” Nucleic Acids Research 40 (3).
Chicago author-date (all authors)
Van Nieuwerburgh, Filip, Ryan C Thompson, Jessica Ledesma, Dieter Deforce, Terry Gaasterland, Phillip Ordoukhanian, and Steven R Head. 2012. “Illumina Mate-paired DNA Sequencing-library Preparation Using Cre-Lox Recombination.” Nucleic Acids Research 40 (3).
Vancouver
1.
Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, et al. Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. NUCLEIC ACIDS RESEARCH. 2012;40(3).
IEEE
[1]
F. Van Nieuwerburgh et al., “Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination,” NUCLEIC ACIDS RESEARCH, vol. 40, no. 3, 2012.
@article{2941861,
  abstract     = {Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.},
  articleno    = {e24},
  author       = {Van Nieuwerburgh, Filip and Thompson, Ryan C and Ledesma, Jessica and Deforce, Dieter and Gaasterland, Terry and Ordoukhanian, Phillip and Head, Steven R},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {GENOMES},
  language     = {eng},
  number       = {3},
  pages        = {8},
  title        = {Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination},
  url          = {http://dx.doi.org/10.1093/nar/gkr1000},
  volume       = {40},
  year         = {2012},
}

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