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  • Which coverage for resequencing genome

    hey, I would like to sequence a genome (~800 MB). We have already the genome of the same species but different strain sequenced with 90x. Which coverage is recommended for resequencing genomes on a hiseq? I would like to identify snps, structural variations, genome rearangements (....) afterwards.
    thanks
    Alex

  • #2
    I suppose that means you have a reference sequence. Then I think 30x is enough if you use PCR-free kit. But most likely you don't have 1-2ug DNA, then 60x is more appropriate. If your genome is AT-rich, you might want to need to do some special treatment.

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    • #3
      I have another question regarding the resequencing project. What methods are commonly applied to subsequenctly assemble the genome when a related reference genome is available. I found velvet (columbus variante) and samtools also provide also a function for assembling mapped reads (mpileup). Is there a standard program for assembling genomes using reference based approaches?
      Many thanks in advance.
      Alex

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