https://github.com/ababaian/serratus

Ultra-deep search for novel viruses
https://github.com/ababaian/serratus

aws bioinformatics coronavirus covid19 open-science sars-cov-2

Last synced: about 11 hours ago
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Ultra-deep search for novel viruses

• Host: GitHub
• URL: https://github.com/ababaian/serratus
• Owner: ababaian
• License: gpl-3.0
• Created: 2020-03-02T23:38:02.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2023-03-29T17:16:28.000Z (over 1 year ago)
• Last Synced: 2024-12-18T06:34:38.575Z (8 days ago)
• Topics: aws, bioinformatics, coronavirus, covid19, open-science, sars-cov-2
• Language: Jupyter Notebook
• Homepage: http://serratus.io
• Size: 6.88 MB
• Stars: 262
• Watchers: 20
• Forks: 34
• Open Issues: 38
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# Serratus

Serratus is a collaborative Open Science project for ultra-rapid discovery of all viruses.

#### Paper: [Petabase-scale sequence alignment catalyses viral discovery](https://www.nature.com/articles/s41586-021-04332-2)

[![Serratus Mountain in Squamish, BC. Canada](https://github.com/ababaian/serratus/wiki/img/splash.png)](https://www.biorxiv.org/content/10.1101/2020.08.07.241729v1)

### Background

_Forewarned is Forearmed._

Our primary goal is to generate the viral data to accelerate the global research efforts in fighting emerging pathogens. We are re-analyzing all RNA-seq, meta-genomics, meta-transcriptomics and environmental sequencing data in the NCBI Short Read Archive to discover new viruses. That is **>6 million biological samples** or >10 petabases of sequencing data.

### Contribute to Serratus

The `Serratus` team is actively looking to collaborate with all scientists and developers.

- See: [CONTRIBUTING.md](CONTRIBUTING.md)

- Join the [`Serratus Slack`](mailto:[email protected]?subject=Joining%20the%20Serratus%20slack&body=Hello%20I%20would%20like%20to%20join%20the%20Serratus%20chat.%20Thanks!) to chat / ask a question.

# Serratus Usage

Learn more on the [Serratus Wiki](https://github.com/ababaian/serratus/wiki/)

### [Serratus Data Explorer](https://serratus.io)

### [palmID: RdRP search](https://serratus.io/palmid)

### [How To: Finding Novel Viruses](https://github.com/ababaian/serratus/wiki/Find_novel_viruses)

### [Accessing Raw Data](https://github.com/ababaian/serratus/wiki/Access-Data-Release) 

### [Cloud Architecture](https://github.com/ababaian/serratus/wiki/Architecture-and-Pipeline)

### [Serratus CLI Usage](https://github.com/ababaian/serratus/wiki/Running-Serratus)

# Data Release Policy

Our primary goal is to generate the viral data to accelerate the global research efforts in fighting emerging pathogens. To achieve this:

- All software development is open-source and freely available (GPLv3)

- All data, raw and processed, will be freely and immediatly available in the public domain in accordance with the [INSDC Policy](https://www.insdc.org/policy/).

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## [About The Team](CONTRIBUTORS.md)