Applications	GS-FLX	GS-FLX+	HiSeq2000	MiSeq
Performance	Read number (million)	1.3	1.3	6000	12
	Read length (bp)	~400	> 500	1X50~2x100	1X36~2x150
	Throughput per plate	360~560Mb	500~800Mb	75GB~300GB	440Mb~4.6Gb
	Physical run type	1/2,1/4,1/8	1/2,1/4,1/8	8 lanes	1 lane
Technology	Running time (Instrument + Primary analysis1)	10 hours+1day	20 hours+2 days	(up to2) 12day+3days	(up to3) 27 hours +2 hours
Library Type	multiplexing	up to 12 MIDs4	up to 12 MIDs	up to 24 IDX5	up to 96 IDX6
	Shotgun library
	Mate Pair library	3kb,8kb,20kb		up to 5kb
	Amplicon library

• 1. Primary analysis means basic analysis only (raw data, base calling and assembly)
• 2. Paired read/run (2x100bp) base
• 3. Paired read/run (2x150bp) base
• 4. MIDs is Multiplex Identifiers defined by Roche Technical Bulletin (TCB No. 005-2009)
• 5. IDX is Index barcodes defined by Roche Technical Bulletin (Cat. No. GABC0950)
• 6. MiSeq multiplexing is available with Nextera Sample prep kit only