There are numerous Next-Generation sequencing platforms available (Roche 454, Illumina, Ion Torrent, Applied Biosystems, PacBio, etc). Each has its own strengths and weaknesses that lead to a segmentation of uses by application. At Cofactor, platform choice and optimization is for us to worry about. All you have to do is describe your research question to us. We'll design your project to choose an optimal platform (or combination of platforms) that minimizes your total fiscal impact without sacrificing the quality of the data or results.
The Roche/454 with Titanium chemistry has the longest reads at up to 1 Kbp, produces the most contiguous assemblies and can phase SNPs or other features into blocks. Errors occur mostly at the ends of longer homopolymers (same- nucleotide stretches). Mate-pair libraries can be constructed of many insert sizes (8kb - 20kb) but halve the read length for each end and have a low efficiency.
The Illumina has shorter reads at 36-150bp but produces up to 200 million reads per lane (8 or 16 lanes possible on a HiSeq 2000). The Illumina has the highest *raw* quality scores and its errors are mostly substitutions. All reads are the same length. Paired-end reads with a variety of insert sizes are possible with high efficiency and double the output of the machine by duplicating the read length on each end. Paired-end Illumina reads are suitable for de novo assemblies, especially in combination with the 454. The large number of reads makes the Illumina appropriate for de novo transcriptome studies with simultaneous discovery and quantification of RNAs at qRT-PCR accuracy.
The Applied Biosystems SOLiD has the shortest read length. As with the Illumina, Mate-Pairs double the output by duplicating the read length on each end, and the SOLiD supports a variety of insert lengths like the 454. The SOLiD can also run 2 slides at once to again double the output. SOLiD has the lowest *raw* base qualities but the highest processed base qualities when using a reference due to its 2-base encoding. The new IonPGMTM Personal Genome Machine made by Ion Torrent, a part of Life Technologies, employs a method of sequencing based on the detection of hydrogen ions released during polymerization of DNA. The Ion torrent generates reads of 100 -200 base pairs with data ranging from 10Mb to 1Gb based on the chip used. The 314 chip generates 10Mb, 316 generates 100Mb and 318 chip - 1Gb.The major benefits of ion semiconductor sequencing are rapid sequencing speed and affordable cost.