https://github.com/ssi-dk/bifrost_sp_cdiff

Cdiff related analysis for the SOFI platform.
https://github.com/ssi-dk/bifrost_sp_cdiff

bifrost cdiff sofi typing

Last synced: about 1 month ago
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Cdiff related analysis for the SOFI platform.

• Host: GitHub
• URL: https://github.com/ssi-dk/bifrost_sp_cdiff
• Owner: ssi-dk
• Created: 2024-06-17T09:33:05.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2024-06-20T10:41:16.000Z (6 months ago)
• Last Synced: 2024-06-21T01:26:11.382Z (6 months ago)
• Topics: bifrost, cdiff, sofi, typing
• Language: Python
• Homepage:
• Size: 9.77 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# bifrost_sp_cdiff

This component runs given a sample_id already added into the bifrostDB. If the sample is registered as *Clostridiodes difficile*, it should pull the paired reads, the contigs, and do the typing according to [cdiff_fbi](https://github.com/ssi-dk/cdiff_fbi)

## How to launch

```bash

git clone https://github.com/ssi-dk/bifrost_sp_cdiff.git

cd bifrost_sp_cdiff

bash install.sh -i LOCAL

conda activate bifrost_sp_cdiff_vx.x.x

export BIFROST_INSTALL_DIR='/your/path/'

BIFROST_DB_KEY="/your/key/here/" python -m bifrost_sp_cdiff -h

```