cgmlst-bacterial-genome/main

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Workflow Type: Galaxy

This workflow performs core genome multilocus sequence typing (cgMLST) on contigs corresponding to one bacterial genome to characterize bacterial strains using curated reference schemes.

SEEK ID: https://workflowhub.eu/workflows/2055?version=2

Inputs

ID Name Description Type
Bacterial genome contigs #main/Bacterial genome contigs The input for this workflow is a single FASTA file containing contigs of one bacterial genome.
  • File
Reference Allele Scheme #main/Reference Allele Scheme Reference Allele Scheme (from pubMLST, BIGSdb, Enterobase, or cgMLST.org) that will be used by CoreProfiler to compare the contigs to and identify corresponding alleles.
  • string

Steps

ID Name Description
2 CoreProfiler Identifies alleles in contigs by comparing them to a reference allele scheme by detecting both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach. toolshed.g2.bx.psu.edu/repos/iuc/coreprofiler_allele_calling/coreprofiler_allele_calling/2.0.0+galaxy2
3 ToolDistillator extraction Extracts results from tool outputs and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.5+galaxy1
4 ToolDistillator summarize Summarizes several ToolDistillator JSON files into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.5+galaxy1

Outputs

ID Name Description Type
CoreProfiler allele calling report #main/CoreProfiler allele calling report n/a
  • File
Extracted cgMLST results by ToolDistillator #main/Extracted cgMLST results by ToolDistillator n/a
  • File
Information about temporary alleles found by CoreProfiler #main/Information about temporary alleles found by CoreProfiler n/a
  • File
Newly detected alleles by CoreProfiler #main/Newly detected alleles by CoreProfiler n/a
  • File
Summarized cgMLST ToolDistillator results #main/Summarized cgMLST ToolDistillator results n/a
  • File

Version History

v1.1 (latest) Created 13th Mar 2026 at 03:02 by WorkflowHub Bot

Updated to v1.1


Frozen v1.1 037b1e1

v1.0 (earliest) Created 21st Jan 2026 at 03:01 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 10c7ab1
help Creators and Submitter
Creators
Additional credit

abromics-consortium

Submitter
License
GNU General Public License v3.0 or later (GPL-3.0-or-later)
Activity

Views: 732   Downloads: 4375   Runs: 1

Created: 21st Jan 2026 at 03:01

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