---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-04-19 23:41:39+00:00
layout: post
slug: kmer-estimation-kmergenie-tweaks-on-geoduck-sequence-data
title: 'Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data '
categories:
  - 2018
  - Geoduck Genome Sequencing
tags:
  - geoduck
  - kmer
  - kmer genie
  - mox
  - Panopea generosa
---

Earlier today, [I ran kmergenie on our all of geoduck DNA sequencing data](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-19-kmer-estimation-kmergenie-on-geoduck-sequence-data-default-settings/) 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







  * Diploid



  * Slurm script: [20180419_kmergenie_diploid_geoduck_slurm.sh](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_geoduck/20180419_kmergenie_diploid_geoduck_slurm.sh)






###### Run 2







  * Diploid


  * k 301



  * Slurm script: [20180419_kmergenie_diploid_k301_geoduck_slurm.sh](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_k301_geoduck/20180419_kmergenie_diploid_k301_geoduck_slurm.sh)






##### Results:





Output folders:





  * [20180419_kmergenie_diploid_geoduck/](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_geoduck/)



  * [20180419_kmergenie_diploid_k301_geoduck/](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_k301_geoduck/)






Slurm output files:





  * [20180419_kmergenie_diploid_geoduck/slurm-162003.out](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_geoduck/slurm-162003.out)



  * [20180419_kmergenie_diploid_k301_geoduck/slurm-162004.out](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_k301_geoduck/slurm-162004.out)






Kmer histogram (HTML) reports:





  * [20180419_kmergenie_diploid_geoduck/histograms_report.html](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_geoduck/histograms_report.html)



  * [20180419_kmergenie_diploid_k301_geoduck/histograms_report.html](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_k301_geoduck/histograms_report.html)






#### Diploid





![](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_geoduck/20180419_kmergenie_diploid_geoduck.png)

  

  




#### Diploid, k 301



![](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_diploid_k301_geoduck/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.