Can I use Abyss assemble a huge genome using limit RAM?

Question

[nifei1998]

Hi, guys. I have almost 300G paired-end (150bp) Illumina short reads and my server has 64 cores and 500G RAM. Can I use Abyss assemble it? The genome size is about 4G.

Thanks!

[h.mon]

You can certainly try. How many reads is this? What is you insert size? Did you calculate the sequencing coverage?

[benv]

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.

[nifei1998]

Thanks for you advise. I will try.