---
# System prepended metadata

title: Acquiring Plastid genes from NGS Data
tags: [RADSeq, GBS, HybSeq]

---

# Acquiring Plastid genes from NGS Data

---
###### tags: `HybSeq` `RADSeq` `GBS`
author: Dylan Cohen
---
This will help users retrieve and align partial to full choroplasts. 
(Note Plastid and Chloroplast are the same)
****************
Overview:

1. Acquire reference and prepare file
2. Assemble raw (filtered/cleaned) reads to reference
 
 ## TO CONSIDER:
There are many different programs to assemble genomes/reads to genes (GetOrganelle, Fast-Plast, RADOrgminer, Hybpiper, PHYLUCE etc)
 





##  WORK IN PROGRESS




