Kmer Estimation – Kmergenie (k 301) on Geoduck Sequence Data

Continuing the quest for the ideal kmer size to use for our geoduck assembly.

The previous two runs with kmergenie using the diploid setting were no good.

So, this time, I simply increased the maximum kmer size to 301 and left all other settings as default. I’m hoping this is large enough to produce a smooth curve, with a maximal value that can be determined from the output graph.

The job was run on our Mox HPC node.


Output folder:

Slurm output file:

Kmer histogram (HTML) reports:

Well, the graph is closer to what we’d expect, in that it appears to reach a zenith, but after that plateau, we see a sharp dropoff, as opposed to a gradual dropoff that mirrors the left half. Not entirely sure what the implications for this are, but I’ll go ahead an run SparseAssembler using a kmer size of 131 and see how it goes.

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