Tag Archives: kmer

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.


Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data

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

Output folders:

Slurm output files:

Kmer histogram (HTML) reports:


Diploid, k 301

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.


Kmer Estimation – Kmergenie on Geoduck Sequence Data (default settings)

After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really know how to decide, particularly since this assembly consisted of mixed read lenghts (50bp and 100bp). So, I ran kmergenie on all of our geoduck (Panopea generosa) sequencing data in hopes of getting a kmer determination to apply to my next assembly.

The job was run on our Mox HPC node.

Slurm script: 20180419_kmergenie_geoduck_slurm.sh

Input files list (needed for kmergenie command – see Slurm script linked above): geoduck_fastq_list.txt


Output folder: 20180419_kmergenie_geoduck/

Slurm output file: 20180419_kmergenie_geoduck/slurm-161551.out

Kmer histograms (HTML): 20180419_kmergenie_geoduck/histograms_report.html

Screen cap from Kmer report:

This data estimates the best kmer size for this data to be 121.

However, based on the kmergenie documentation, this is likely to be inaccurate. This inaccuracy is based on the fact that our kmer graph should be concave. Our graph, instead, is only partial – we haven’t reached a kmer size where the number of kmers is decreasing.

As such, I’ll try re-running with a different maximum kmer settting (default max is 121).


NovaSeq Assembly – Trimmed Geoduck NovaSeq with Meraculous

Attempted to use Meraculous to assemble the trimmed geoduck NovaSeq data.

Here’s the Meraculous manual (PDF).

After a bunch of various issues (running out of hard drive space – multiple times, config file issues, typos), I’ve finally given up on running meraculous. It failed, again, saying it couldn’t find a file in a directory that meraculous created! I’ve emailed the authors and if they have an easy fix, I’ll implement it and see what happens.

Anyway, it’s all documented in the Jupyter Notebook below.

One good thing came out of all of it is that I had to run kmergenie to identify an appopriate kmer size to use for assembly, as well as estimated genome size (this info is needed for both meraculous and SOAPdeNovo (which I’ll be trying next)):

kmergenie output folder: http://owl.fish.washington.edu/Athaliana/20180125_geoduck_novaseq/20180206_kmergenie/
kmergenie HTML report (doesn’t display histograms for some reason): 20180206_kmergenie/histograms_report.html
kmer size: 117
Est. genome size: 2.17Gbp

Jupyter Notebook (GitHub): 20180205_roadrunner_meraculous_geoduck_novaseq.ipynb