Name: wrangling-genomics
Owner: Data Carpentry
Description: null
Created: 2015-03-24 17:51:36.0
Updated: 2017-12-18 08:34:21.0
Pushed: 2017-12-04 20:15:56.0
Homepage: http://www.datacarpentry.org/wrangling-genomics/
Size: 64562
Language: Python
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| James Allen | 2015-01-26 10:00:10.0 | 2 |
| Peter Cock | 2017-11-21 11:19:02.0 | 4 |
| Piotr Banaszkiewicz | 2015-02-18 19:30:08.0 | 4 |
| Jonah Duckles | 2016-09-26 20:09:00.0 | 1 |
| W. Trevor King | 2017-01-23 22:54:50.0 | 1 |
| Rémi Emonet | 2016-09-05 17:28:26.0 | 5 |
| Karen Cranston | 2017-01-16 19:48:34.0 | 3 |
| Sheldon McKay | 2015-07-31 21:57:39.0 | 38 |
| Jon Pipitone | 2013-07-27 03:04:21.0 | 2 |
| Abigail Cabunoc Mayes | 2014-11-24 20:23:52.0 | 26 |
| Tracy Teal | 2017-11-18 20:24:07.0 | 14 |
| Greg Wilson | 2017-01-18 12:27:55.0 | 125 |
| Lex Nederbragt | 2017-11-15 10:57:33.0 | 13 |
| Fotis E. Psomopoulos | 2018-02-01 11:00:57.0 | 47 |
| Raniere Silva | 2017-05-10 10:05:10.0 | 50 |
| Bill Mills | 2014-12-31 06:06:23.0 | 1 |
| synesthesiam | 2014-01-12 23:08:50.0 | 2 |
| Gabriel A. Devenyi | 2016-07-21 13:52:21.0 | 1 |
| Nick Young | 2017-01-31 21:19:36.0 | 2 |
| Ian Carroll | 2016-12-31 01:49:20.0 | 1 |
| Lisa Johnson | 2018-01-25 21:48:58.0 | 1 |
| Ming Tang | 2017-11-14 20:37:49.0 | 6 |
| Chris Hamm | 2015-03-26 01:02:51.0 | 2 |
| Kate Crosby | 2017-06-22 20:01:46.0 | 14 |
| François Michonneau | 2017-05-04 15:58:52.0 | 36 |
| Pete | 2017-11-21 22:08:33.0 | 24 |
| Dev Paudel | 2017-05-31 17:01:15.0 | 1 |
| Jason Williams | 2016-05-29 18:50:43.0 | 28 |
| Hadrien Gourlé | 2017-06-22 20:32:57.0 | 11 |
| Adam Thomas | 2016-05-25 21:17:47.0 | 3 |
| HLindsay | 2016-12-04 16:17:05.0 | 3 |
| dbmarchant | 2015-03-25 15:26:06.0 | 5 |
| Luis Avila | 2017-06-22 18:03:40.0 | 1 |
| Gaius | 2017-08-02 05:03:48.0 | 7 |
| Maxim Belkin | 2016-12-14 17:40:19.0 | 2 |
| EvanWill | 2016-09-23 04:52:27.0 | 2 |
| gtehennepe | 2017-11-15 14:48:39.0 | 1 |
| Erin Becker | 2017-12-04 19:44:48.0 | 91 |
| Kari L. Jordan, PhD | 2017-01-12 16:26:57.0 | 2 |
| Taylor Reiter | 2018-01-31 16:09:57.0 | 4 |
| NielInfante | 2017-06-22 20:34:32.0 | 12 |
Other Committers
| User | Most Recent Commit | # Commits | |
|---|---|---|---|
| Raniere Silva | ra092767@ime.unicamp.br | 2013-10-01 15:00:47.0 | 2 |
| Raniere Silva | raniere@ime.unicamp.br | 2015-05-02 11:11:13.0 | 33 |
| Sheldon McKay | sheldon.mckay@gmail | 2015-03-25 11:23:35.0 | 3 |
| Timothée Poisot | tim@poisotlab.io | 2014-11-14 00:38:43.0 | 1 |
| Vasilis Lenis | vpl@aber.ac.uk | 2016-11-04 11:13:00.0 | 1 |
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”.
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.
All participants should agree to abide by the Data Carpentry Code of Conduct.
Wrangling genomics is authored and maintained by the community.
Please cite as:
Wrangling Genomics. June 2017. http://datacarpentry.github.io/wrangling-genomics/.