---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-09-18 21:50:13+00:00
layout: post
slug: genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-2
title: Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon
categories:
  - 2017
  - Olympia Oyster Genome Sequencing
tags:
  - jupyter notebook
  - miniasm
  - olympia oyster
  - Ostrea lurida
  - PacBio
  - racon
---

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).

Previously, ran the first part of the pipeline: [minimap](https://robertslab.github.io/sams-notebook/posts/2017/2017-09-07-genome-assembly-olympia-oyster-pacbio-minimapminiasmracon/)

This notebook entry just contains the miniasm execution. Will follow with [racon](https://robertslab.github.io/sams-notebook/posts/2017/2017-09-18-genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-3/).

Jupyter Notebook (GitHub): [20170918_docker_pacbio_oly_miniasm0.2.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20170918_docker_pacbio_oly_miniasm0.2.ipynb)
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