https://github.com/euphrasiologist/gbs_v2_tassel_5

Shell Scripts for a Genotyping by Sequencing analysis.
https://github.com/euphrasiologist/gbs_v2_tassel_5

Last synced: 12 days ago
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Shell Scripts for a Genotyping by Sequencing analysis.

• Host: GitHub
• URL: https://github.com/euphrasiologist/gbs_v2_tassel_5
• Owner: Euphrasiologist
• Created: 2020-02-11T12:12:43.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-02-11T22:22:32.000Z (almost 5 years ago)
• Last Synced: 2023-10-20T19:44:43.318Z (over 1 year ago)
• Language: Shell
• Size: 5.86 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Genotyping by Sequencing pipeline

Provided in this repository are shell scripts for a Genotyping by Sequencing analysis. The pipeline used is the Tassel 5 GBS version 2 which can be seen here:

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline

The pipeline is reasonably straighforward and generates eventually a VCF containing genotypes and variants of all the taxa sampled.

All parameters I have used are pretty much the default ones and will eventually be fine tuned.