Author(s): Hillman, David; Pedraza, Mary Ann; Sunkara, Sirisha; Shin, Maria; Froula, Jeff; Chen, Feng; Pennacchio, Len | 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.