In 2006, Solexa released the Genome Analyzer (GA), and in 2007 the company was purchased by Illumina. The sequencer adopts the technol­ogy of sequencing by synthesis (SBS). The library with fixed adaptors is denatured to single strands and grafted to the flowcell, followed by bridge amplification to form clusters which contains clonal DNA fragments. Before sequencing, the library splices into single strands with the help of linearization enzyme [10], and then four kinds of nucleotides (ddATP, ddGTP, ddCTP, ddTTP) which contain different cleavable fluorescent dye and a removable blocking group would complement the template one base at a time, and the signal could be captured by a (charge-coupled device) CCD.

At first, solexa GA output was 1 G/run. Through improvements in poly­merase, buffer, flowcell, and software, in 2009 the output of GA increased to 20 G/run in August (75PE), 30 G/run in October (100PE), and 50 G/run in December (Truseq V3, 150PE), and the latest GAIIx series can attain 85 G/run. In early 2010, Illumina launched HiSeq 2000, which adopts the same sequencing strategy with GA, and BGI was among the first globally to adopt the HiSeq system. Its output was 200 G per run initially, improved to 600 G per run currently which could be finished in 8 days. In the fore­seeable future, it could reach 1 T/run when a personal genome cost could drop below $1 K. The error rate of 100PE could be below 2% in average after filtering (BGI’s data). Compared with 454 and SOLiD, HiSeq 2000 is the cheapest in sequencing with $0.02/million bases (reagent counted only by BGI). With multiplexing incorporated in P5/P7 primers and adapters, it could handle thousands of samples simultaneously. HiSeq 2000 needs (HiSeq control software) HCS for program control, (real-time analyzer software) RTA to do on-instrument base-calling, and CASAVA for sec­ondary analysis. There is a 3 TB hard disk in HiSeq 2000. With the aid of Truseq v3 reagents and associated softwares, HiSeq 2000 has improved much on high GC sequencing. MiSeq, a bench top sequencer launched in 2011 which shared most technologies with HiSeq, is especially convenient for amplicon and bacterial sample sequencing. It could sequence 150PE and generate 1.5 G/run in about 10 hrs including sample and library prepa­ration time. Library preparation and their concentration measurement can both be automated with compatible systems like Agilent Bravo, Hamilton Banadu, Tecan, and Apricot Designs.