The iScan Reader, a high-performance optical detection system, not only greatly reduces the scanning time required but also provides high quality with a high level of reproducibility. At RIKEN GENESIS we use the LIMS system, iScan and Autoloader 2 to enable efficient sample tracking, operation management, and data calculation for even large-scale projects. Using the iScan Reader and Autoloader 2 means a scanning time of 7 min for each sample on a 610-Quad chip, so that 288 samples and approximately 170 million SNPs can be scanned automatically overnight.