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Improvements to the Illumina Sequencing System and New Applications

  • Author(s): Hillman, David
  • Pedraza, Mary Ann
  • Sunkara, Sirisha
  • Shin, Maria
  • Froula, Jeff
  • Chen, Feng
  • Pennacchio, Len
  • et al.
Abstract

Next Generation sequencing products and procedures for the Illumina platform were evaluated, several of which immediately benefited JGI users. Paired end-reads of 35 bases each have become routine on our new GAii instruments with output in excess of 6 billion bases per run. Single reads have been used for polishing finished genomic sequence data for over 2 years, and collaborative work has progressed to include genomic SNP detection, expression analysis for eukaryotes and prokaryotes, and ChIP DNA sequencing. Paired End-Reads have been particularly useful for SNP detection. Our beta testing activities include positive results for barcode libraries (indexing) using Illumina's 3 primer scheme, large-gap libraries produced several ways, and accurate 75 base read-length. Key technologies include improvements to the instruments, reagents, software, and information management tools.

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