---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-09-07 21:39:38+00:00
layout: post
slug: genome-assembly-olympia-oyster-pacbio-minimapminiasmracon
title: Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon
categories:
  - 2017
  - Olympia Oyster Genome Sequencing
tags:
  - jupyter notebook
  - minimap
  - olympia oyster
  - Ostrea lurida
  - PacBio
---

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 initial minimap execution. Followed up with [miniasm](https://robertslab.github.io/sams-notebook/posts/2017/2017-09-18-genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-2//robertslab.github.io/sams-notebook/2017/09/18/genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-3/).

Jupyter Notebook (GitHub): [20170907_docker_pacbio_oly_minimap2.ipynb](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20170907_docker_pacbio_oly_minimap2.ipynb)

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