tovanadler / start-here

Documentation for the Google Genomics cookbook.

Welcome to the Google Genomics GitHub Organization!

New to Google Genomics?

• Watch this codelab walkthrough:
  
• Try a few queries on public genomic data using Google BigQuery.

If you are ready to start coding, take a look at the list below. But if you are looking for a task-oriented list (e.g., "how do I analyze variants with Google Genomics"), a better place to start is the Google Genomics Cookbook.

What You'll Find on GitHub

Interactive Data Analysis Samples and Tools

• getting-started-bigquery Example queries to show how to get started with genomic data in BigQuery.

• codelabs Codelabs demonstrating usage of several tools and systems on genomic data.

• bigquery-examples Advanced BigQuery examples on genomic data.

• api-client-java A command line tool for Google Genomics API queries.

• api-client-r An R package for Google Genomics API queries.

• gatk-tools-java Tools for using Picard and GATK with the Google Genomics API.

Cluster Computing Data Analysis Samples

• dataflow-java Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

• spark-examples Apache Spark jobs such as Principal Coordinate Analysis.

Working with the Google Genomics API

• getting-started-with-the-api Examples of how to get started with the Google Genomics API in many languages.

• api-provider-local-java An implementation of the Global Alliance Reads API which reads data from local BAM files.

Data Visualization Application Samples

• api-client-javascript A simple web application that demonstrates how javascript can be used to fetch data from the Google Genomics APIs.

• api-client-android A sample Android app that calls the Google Genomics API.

• api-client-python Google AppEngine implelmentation of a simple genome browser that pulls data from the Google Genomics API.

• api-client-r An R package for Google Genomics API queries.

• See the Shiny example.

• See the ggbio example.

Data Analysis Application Samples

• denovo-variant-caller-java A de novo variant caller which uses information from a mother, father and child trio with a bayesian inference method.

Miscellaneous

• gce-images Scripts that create a Google Compute Engine image containing a set of popular genomics software.

• utils-java Common Java files for Google Genomics integrations.

Documentation

• See https://cloud.google.com/genomics to understand what Google Genomics is and how to get started.
• See http://googlegenomics.readthedocs.org for an incrementally growing task-oriented cookbook.
• See the README in each GitHub repository for specifics about the code.