https://github.com/pasted/targeted_sequencing_pipeline

Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab.
https://github.com/pasted/targeted_sequencing_pipeline

bioinformatics bioinformatics-pipeline

Last synced: 5 months ago
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Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab.

• Host: GitHub
• URL: https://github.com/pasted/targeted_sequencing_pipeline
• Owner: pasted
• License: other
• Created: 2015-12-24T12:54:22.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2018-06-12T12:33:38.000Z (about 8 years ago)
• Last Synced: 2025-05-16T12:39:40.984Z (about 1 year ago)
• Topics: bioinformatics, bioinformatics-pipeline
• Language: HTML
• Homepage:
• Size: 402 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# Targeted sequencing pipeline

Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab. 

Created by Garan Jones g.jones@exeter.ac.uk

Ruby class based pipeline with Excel outputs. 

Requires following software to run

* Ruby 1.9+

The following can be configured separately (config.yaml):

* Java 1.8

* GenomeAnalysisTK-3.6.0

* alamut-batch-1.5.2

* picard-tools-2.5.0

* bwa-0.7.15

* R-3.2.0

###Common Errors