swc-uiuc/wrangling-genomics

Name: wrangling-genomics

Owner: Software Carpentry at Urbana-Champaign

Description: The original wrangling-genomics lesson edited to accommodate Biocluster usage rather than AWS.

Created: 2018-02-19 21:53:58.0

Updated: 2018-02-19 22:27:15.0

Pushed: 2018-02-22 15:20:31.0

Homepage: http://swc-uiuc.github.io/wrangling-genomics/

Size: 64613

Language: Python

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README

Wrangling Genomics

Lesson for quality control and wrangling genomics data. This repository is maintained by Josh Herr, Ming Tang, Lex Nederbragt, and Fotis Psomopoulos.

Amazon public AMI for this tutorial is “dataCgen-qc”.

Background

Wrangling genomics trains novice learners on a variant calling workflow. Participants will learn how to evaluate sequence quality and what to do if it is not good. We will then cover aligning reads to a genome, and calling variants, as well as discussing different file formats. Results will be visualized. Finally, we will cover how to automate the process by building a shell script.

This lesson is part of the Data Carpentry Genomics Workshop.

Contribution

• Make a suggestion or correct an error by raising an Issue.

Code of Conduct

All participants should agree to abide by the Data Carpentry Code of Conduct.

Authors

Wrangling genomics is authored and maintained by the community.

Citation

Please cite as:

Wrangling Genomics. June 2017. http://datacarpentry.github.io/wrangling-genomics/.