Question: Can I use Abyss assemble a huge genome using limit RAM?
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You can certainly try. How many reads is this? What is you insert size? Did you calculate the sequencing coverage?
It is certainly worth a try. 500GB RAM is in the right ballpark for a genome of that size.
The memory usage depends on the number of distinct k-mers in your sequencing data, which depends on genome size, sequencing coverage, and sequencing error rate.
You can reduce the memory requirement by adding the quality trimming option (e.g.
q=15) to your abyss-pe command. That will trim the tails of the reads and remove a lot of the error k-mers.Thanks for you advise. I will try.