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Old 09-16-2014, 09:48 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I highly recommend subsampling that data; you have way too much to get a good assembly. Hard to say how much you need since mito vary in size. I'd start by subsampling by a factor of 200 and assembling again to get a better idea of how big the genome is (or you could estimate the size from a kmer frequency plot). Then, if you want to assemble with Velvet, subsample again or normalize to around 40x coverage.

You can subsample paired reads with my reformat tool, which will keep the pairing intact.
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