---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-04-19 21:28:52+00:00
layout: post
slug: kmer-estimation-kmergenie-on-geoduck-sequence-data-default-settings
title: Kmer Estimation - Kmergenie on Geoduck Sequence Data (default settings)
categories:
  - 2018
  - Geoduck Genome Sequencing
tags:
  - geoduck
  - kmer
  - kmer genie
  - mox
  - Panopea generosa
---

After the [last SparseAssembler assembly completed](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-05-genome-assembly-sparseassembler-geoduck-genomic-data-kmer101/), 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](https://kmergenie.bx.psu.edu/README) 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](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/20180419_kmergenie_geoduck_slurm.sh)

Input files list (needed for kmergenie command - see Slurm script linked above): [geoduck_fastq_list.txt](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/geoduck_fastq_list.txt)



##### Results:



Output folder: [20180419_kmergenie_geoduck/](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/)

Slurm output file: [20180419_kmergenie_geoduck/slurm-161551.out](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/slurm-161551.out)

Kmer histograms (HTML): [20180419_kmergenie_geoduck/histograms_report.html](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/histograms_report.html)

Screen cap from Kmer report:

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

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

However, based on the [kmergenie documentation](https://owl.fish.washington.edu/Athaliana/20180419_kmergenie_geoduck/histograms_report.html#advhelp), 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).
