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  • Hybrid assembly with Illumina and SOLiD data

    Hi,

    I am trying to assemble a genome from using SOLiD and Illumina paired end data. I have about 30x coverage from Illumina and a similar level from SOLiD. What would be a good assembly program for this? One point I was wondering was that color space assemblers like velvet do not take base space output, so would be okay to convert base space to colorspace? Color space to base space is not recommended as any errors will propagate throughout the read but the other way round should be fine.

  • #2
    hi,
    if you convert base to color space you will have 2 consecutive color space errors for each illumina sequencing errors instead of only one in your color space reads. Not sure this is a good idea to then gathered both set into one to feed to assemblers. I see some projects concerning hybrid assembly with llumina and 454 reads but i've no idea about treating hybrid assembly with solexa and SOLiD.
    best regards,
    kevin.

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