https://github.com/hammerlab/bdgenomics-notebook
https://github.com/hammerlab/bdgenomics-notebook
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/hammerlab/bdgenomics-notebook
- Owner: hammerlab
- Created: 2014-04-12T22:58:04.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2014-05-06T07:35:26.000Z (about 12 years ago)
- Last Synced: 2025-11-20T10:06:29.484Z (7 months ago)
- Size: 250 KB
- Stars: 2
- Watchers: 11
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# A Walk Through Big Data Genomics Data Types
You can view this notebook online via iPython's nbviewer [here](http://nbviewer.ipython.org/github/hammerlab/bdgenomics-notebook/blob/master/Big-Data-Genomics-Tutorial.ipynb). (Note, for some reason raw text fields lose formatting when viewed this way: downloading and locally running this notebook makes viewing those fields easier.)
This [iPython notebook](http://ipython.org/) is meant to introduce you to the various datatypes used with the ADAM stack to process next-generation sequencing (NGS) data.
To get up and running, simply start the iPython notebook in this directory with `ipython notebook` and open the notebook.
ADAM uses [Avro](http://avro.apache.org/) to specify its datatypes, and thus you must have the `avro` Python package installed in order to run this tutorial. The easiest way to do this is with `pip install avro`.