Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

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Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an ... continued below

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Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A. & Chen, Feng May 27, 2010.

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Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an overall experimental strategy, primer design algorithm and initial results.

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  • Sequencing, Finishing and Analysis in the Future Meeting, San Fe, New Mexico, June 2 - 4, 2010

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  • Report No.: LBNL-3659E-Poster
  • Grant Number: DE-AC02-05CH11231
  • DOI: 10.2172/985324 | External Link
  • Office of Scientific & Technical Information Report Number: 985324
  • Archival Resource Key: ark:/67531/metadc1013578

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • May 27, 2010

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  • Oct. 14, 2017, 8:36 a.m.

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  • Oct. 17, 2017, 6:13 p.m.

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Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A. & Chen, Feng. Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing, report, May 27, 2010; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc1013578/: accessed January 19, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.