---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-09-18 22:02:49+00:00
layout: post
slug: genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-3
title: Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon
categories:
  - 2017
  - Miscellaneous
---

In this [GitHub Issue](https://github.com/RobertsLab/project-olympia.oyster-genomic/issues/29), Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

I followed the pipeline described by this paper: [https://matzlab.weebly.com/uploads/7/6/2/2/76229469/racon.pdf](http://matzlab.weebly.com/uploads/7/6/2/2/76229469/racon.pdf).

This notebook entry just contains the racon execution. This produced this assembly:

[https://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta](http://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta)

All intermediate files generated from this pipeline are here:

[https://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/](http://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/)

I'll put together a TL;DR post that provides an overview of the pipeline and an assessment of the final assembly.

Previously ran [minimap](https://robertslab.github.io/sams-notebook/posts/2017/2017-09-07-genome-assembly-olympia-oyster-pacbio-minimapminiasmracon/)
 and then [miniasm](https://robertslab.github.io/sams-notebook/posts/2017/2017-09-18-genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-2/).

Jupyter Notebook (GitHub): [20170918_docker_pacbio_oly_racon0.5.0.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20170918_docker_pacbio_oly_racon0.5.0.ipynb)

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