Sam’s Notebook:Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data

0000-0002-2747-368X

Earlier today, I ran kmergenie on our all of geoduck DNA sequencing data to see what it would spit out for an ideal kmer setting, which I would then use in another assembly attempt using SparseAssembler; just to see how the assembly might change.

The output from that kmergenie run suggested that the ideal kmer size exceeded the default maximum (k = 121), so I decided to run kmergenie a few more times, with some slight changes.

All jobs were run on our Mox HPC node.

Run 1
Run 2
Results:

Output folders:

Slurm output files:

Kmer histogram (HTML) reports:

Diploid

20180419_kmergenie_diploid_geoduck.png

Diploid, k 301

20180419_kmergenie_diploid_k301_geoduck.png

Okay, well, these graphs clearly show that the diploid setting is no good.

We should be getting a nice, smooth, concave curve.

Will try running again, without diploid setting and just increasing the max kmer size.

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