Currently, Roche 454 has a unique selling proposition in providing the only sequencing technology on the market delivering long reads with high accuracy at the same time. Just last year Roche 454 launched the new GS FLX+ chemistry delivering reads with a modal read length of up to 700 bp. Long reads are crucial for de novo sequencing of genomes and transcriptomes and for sequencing of amplicons.
The current version of the Illumina MiSeq enables 2x 150 bp paired-end reads and 1.5 – 2 Gbp per run, which is slightly over the output of a typical GS FLX+ run. When working with short insert libraries of 200-250 bp, both paired-end reads will overlap and finally generate one longer read of up to 250 bp.
This read length is still not in a competitive range for Roche 454, but recently Illumina announced the launch of a MiSeq instrument upgrade by the middle of the year. According to Illumina ‘s vice president of marketing, the upgraded instrument will generate 2x 250 bp paired-end reads and up to 7 Gbp of data output. When sequencing short insert libraries with the 2x 250 bp paired-end module, reads with up to 450 bp can be generated. Thus, read length comes again closer to the read length of the Roche FLX+ technology (not to mention the 10x higher data output).
We have to wait and see whether the MiSeq upgrade keeps what Illumina promises, but for me personally it is quite clear, that with the announced specifications, the MiSeq will sooner or later replace Roche 454 sequencing for certain applications. In this light it is very interesting that Roche offered a friendly take over of Illumina this week.