Cofactor genomics on the different NGS platforms

Original post here

They are a commercial company that offers NGS on ABI and Illumina platforms and since this is on their company page I guess its their official stand on what rocks on each platform

Excerpted.

Applied Biosystems SOLiD 3

The Applied Biosystems SOLiD 3 has the shortest but also the highest quantity of reads. The SOLiD produces up to 240 million 50bp reads per slide per end. As with the Illumina, Mate-Pairs produce 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. Because of the number of reads and more advanced library types, we recommend the SOLiD for all RNA and bisulfite sequencing projects.

Solexa/Illumina

The Solexa/Illumina generates shorter reads at 36-75bp but produces up to 160 million reads per run.  All reads are of similar length.  The Illumina has the highest *raw* quality scores and its errors are mostly base substitutions. Paired-end reads with ~200 bp inserts 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 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.

Roche/454 FLX

The Roche/454 FLX with Titanium chemistry generates the longest reads (350-500bp) and the most contiguous assemblies, can phase SNPs or other features into blocks, and has the shortest run times. However, 454 also produces the fewest total reads (~1 million) at the highest cost per base. Read lengths are variable. Errors occur mostly at the ends of long same-nucleotide stretches. Libraries can be constructed with many insert sizes (8kb - 20kb) but at half of the read length for each end and with low efficiency.