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

Component for running seqsero in Bifrost
https://github.com/ssi-dk/bifrost_seqsero

Last synced: 3 days ago
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Component for running seqsero in Bifrost

• Host: GitHub
• URL: https://github.com/ssi-dk/bifrost_seqsero
• Owner: ssi-dk
• License: mit
• Created: 2021-03-23T11:51:32.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-03-08T13:47:55.000Z (8 months ago)
• Last Synced: 2024-03-09T13:40:43.191Z (8 months ago)
• Language: Python
• Size: 50.8 KB
• Stars: 0
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE

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README

        
# bifrost_seqsero

This component is run given a sample id already added into the bifrostDB. If the sample is registered as Salmonella enterica, this will pull the paired_reads and predicts the serotype using Seqsero v1. The output of this is a serotype string and the serotype name according to the Kauffman-White scheme.

## Howto launch

  /bifrost/components/bifrost_seqsero$ docker-compose run bifrost_seqsero

## How to debug

  /bifrost/components/bifrost_seqsero$ docker-compose run --entrypoint=bash bifrost_seqsero