https://github.com/lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
https://github.com/lynnlangit/gcp-for-bioinformatics
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers gcp genomics google google-batch nextflow
Last synced: 10 days ago
JSON representation
GCP for Bioinformatics Researchers
- Host: GitHub
- URL: https://github.com/lynnlangit/gcp-for-bioinformatics
- Owner: lynnlangit
- License: apache-2.0
- Created: 2019-06-06T13:13:19.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-11-25T00:56:07.000Z (5 months ago)
- Last Synced: 2025-04-03T09:08:48.452Z (19 days ago)
- Topics: bioinformatics, bioinformatics-analysis, bioinformatics-pipeline, bioinformatics-researchers, gcp, genomics, google, google-batch, nextflow
- Language: Jupyter Notebook
- Homepage: https://www.youtube.com/playlist?list=PL4Q4HssKcxYvcixWS08UFaYIH7y4IAV0z
- Size: 89.9 MB
- Stars: 258
- Watchers: 15
- Forks: 70
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# Google Cloud Platform (GCP) for Bioinformatics
This repository shows how to use Google Cloud Platform (GCP) public cloud services to scale sets of **bioinformatics data analysis** tasks. This Repo uses cloud best practices for GCP. All examples use **genomic** sample (input) data, tools and pipelines. Use cases included here as examples are called by any and all of the following terms:
- genomic-scale data workflows or pipelines
- bioinformatics primary, secondary or tertiary analysis
- distributed cloud-based batch jobs
This content is intended for researchers - in particular, this guide is for those who are **NEW to working with GCP**. You have a number of options on how to use the materials provided in this course. A summary is shown below left.
This Repo includes content you can read, watch or run:
- 📗 **READ** - one page of this Repo (MD page)
- 📺 **WATCH** - linked YouTube screencasts
- 📙 **RUN** - Jupyter Notebook example
- :octocat: **TRY** - linked GitHub Repos
- 📘 **EXPAND** - linked (external) resources
- 🔍 **SCAN** - search a list in this Repo
NOTE: If you are looking for AWS guidance, see my **'aws-for-bioinformatics'** Repo/Course at [link](https://github.com/lynnlangit/aws-for-bioinformatics)
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### 📺 Click below to WATCH 'Lynn's Welcome Video' (4 min) on YouTube
[](http://www.youtube.com/watch?v=YoFkSVDlN6k "Welcome to GCP for Bioinformatics")
---
### Why would I choose to use a public cloud vendor for bioinformatics?
⭐️ **SAVE MONEY** run (and pay for) scalable analysis jobs only when you need to run them
⭐️ **SAVE TIME** use vendor-managed infrastructure & best-practice patterns for fast repeatable research
📗 **READ** the [FAQ for GCP bioinformatics](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/1_FAQ.md) for this Repo
📕 **READ** Nature article: ["Cloud computing for genomic data analysis and collaboration"](https://www.nature.com/articles/nrg.2017.113)
📗 **READ** the top 4 most [common use cases](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/3_USER-STORIES.md) for using the public cloud for bioinformatics researchers
### Bioinformatics wanting more advanced GCP content?
If you would like to learn **more advanced concepts** (including script examples and patterns) about working with Google Cloud Platform, see my Repo `gcp-essentials` --> [link](https://github.com/lynnlangit/gcp-essentials)
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### New to Bioinformatics?
If you are **NEW to bioinformatics** and have a computational background...
- :octocat: **REVIEW** my bioinformatics concepts tools and terms
- Designed for experienced cloud practioners who are **NEW to Bioinformatics**
- The 'student notes repo' is named `Team Teri` - [link](https://github.com/lynnlangit/TeamTeri#who-is-teri) to 'who is Teri?'
- This Repo includes links to explanations of bioinformatics concepts, tools and platforms - [link](https://github.com/lynnlangit/TeamTeri)
----
### Contibutions
We love contributions! See this [short style guide](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/CONTRIBUTING.md) when making pull requests to this repo.
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