patho_typing

Purpose

Patho_typing is a software for in silico pathogenic typing directly from raw Illumina reads.

Note

Software page: https://github.com/B-UMMI/patho_typing

Input/Output type

  • Input type: FastQ
  • Output type: None

Parameters

  • species: Species name. Must be the complete species name with genus and species, e.g.: ‘Yersinia enterocolitica’.

Published results

  • results/pathotyping/<sample id>: Stores the results of patho_typing in text and tabular format.

Published reports

None.

Default directives

  • cpus: 4
  • memory: 4GB
  • container: ummidock/patho_typing
  • version: 0.3.0-1

Advanced

Reports JSON

typing:
  • pathotyping: <typing result>