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  • solexa vs 454 read length reasons

    Hi I want to know what is the limiting factor of the length of solexa reads and why in 454 it is possible to receive much longer reads?

  • #2
    I can only speculate.

    Signal strength?
    A solexa cluster would contain far fewer amplicons than a 20 um 454 bead.

    Another possibility is just degradation of the template strands over time. A 454 run is over in less than 1 day whereas it takes > 1 week to get out to 100 bases on a solexa. Even if the templates can tolerate the extra abuse time will wreak, there is the issue that every base added in a solexa run is a terminator base and the terminator chemistry must be reversed prior to adding another base. Whereas 454 does not use terminators. It might be that the former generates more Carry-Forward and Incomplete Termination Errors (CAFIE) than the latter.

    Finally, Solexa uses 4 color chemistry whereas the 454 generates all its signals in a single channel. The extra complications involved with color processing may take a toll as well.

    --
    Phillip

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    • #3
      My understanding is that Solexa read length is limited as the flurochromes interfer with the DNA polymerase reducing its efficiency and thus eventually a majority of the strands have been terminated early. On the other hand the flurochrome gives a much stronger signal than the luciferase in 454 allowing more beads to be packed in, thus more sequence.

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      • #4
        Another potential contributor to greater density of the SOLiD & Illumina platforms vs. 454 is that the signal from SOLiD & Illumina is stable, whereas the pyrosequencing approach results in a transient flash. Hence, at some point (though I don't know it has been reached) you are limited by camera resolution, whereas the SOLiD & Illumina can scan multiple images of the slide.

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