Which coverage for resequencing genome

[abastkowska]

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

[ymc]

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.

[abastkowska]

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