https://github.com/datacarpentry/wrangling-genomics

Data Wrangling and Processing for Genomics
https://github.com/datacarpentry/wrangling-genomics

carpentries data-carpentry data-wrangling english genomics lesson programming shell stable

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Data Wrangling and Processing for Genomics

• Host: GitHub
• URL: https://github.com/datacarpentry/wrangling-genomics
• Owner: datacarpentry
• License: other
• Created: 2015-03-24T17:51:36.000Z (almost 11 years ago)
• Default Branch: main
• Last Pushed: 2026-03-10T00:37:38.000Z (9 days ago)
• Last Synced: 2026-03-10T08:10:17.331Z (8 days ago)
• Topics: carpentries, data-carpentry, data-wrangling, english, genomics, lesson, programming, shell, stable
• Language: Shell
• Homepage: https://datacarpentry.org/wrangling-genomics/
• Size: 73.4 MB
• Stars: 73
• Watchers: 22
• Forks: 151
• Open Issues: 51
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.md
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATION
  • Authors: AUTHORS
  • Zenodo: .zenodo.json

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# Wrangling Genomics

Lesson for quality control and wrangling genomics data. This repository is maintained by [Josh Herr](https://github.com/jrherr), [Ming Tang](https://github.com/crazyhottommy), and [Fotis Psomopoulos](https://github.com/fpsom).

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](https://www.datacarpentry.org/) [Genomics Workshop](https://www.datacarpentry.org/genomics-workshop/).

## Contribution

- Make a suggestion or correct an error by [raising an Issue](https://github.com/datacarpentry/wrangling-genomics/issues).

## Code of Conduct

All participants should agree to abide by the [Data Carpentry Code of Conduct](https://www.datacarpentry.org/code-of-conduct/).

## Authors

Wrangling genomics is authored and maintained by the [community](https://github.com/datacarpentry/wrangling-genomics/network/members).

## Citation

Please cite as:

Erin Alison Becker, Taylor Reiter, Fotis Psomopoulos, Sheldon John McKay, Jessica Elizabeth Mizzi, Jason Williams, … Winni Kretzschmar. (2019, June). datacarpentry/wrangling-genomics: Data Carpentry: Genomics data wrangling and processing, June 2019 (Version v2019.06.1). Zenodo. [http://doi.org/10.5281/zenodo.3260609](https://doi.org/10.5281/zenodo.3260609)