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

Ecoli related analysis for the SOFI platform.
https://github.com/ssi-dk/bifrost_sp_ecoli

bifrost ecoli sofi typing

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

• Host: GitHub
• URL: https://github.com/ssi-dk/bifrost_sp_ecoli
• Owner: ssi-dk
• Created: 2024-06-28T08:01:44.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2024-11-11T14:57:11.000Z (about 1 month ago)
• Last Synced: 2024-11-11T15:42:47.487Z (about 1 month ago)
• Topics: bifrost, ecoli, sofi, typing
• Language: Python
• Homepage:
• Size: 54.7 KB
• Stars: 0
• Watchers: 6
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# bifrost_sp_ecoli

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

## How to launch

```bash

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

cd bifrost_sp_ecoli

git submodule init

git submodule update

bash install.sh -i LOCAL

conda activate bifrost_sp_ecoli_vx.x.x

export BIFROST_INSTALL_DIR='/your/path/'

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

```