clermontyping
Tags: escherichia-coli phylogroup typing clermont sample-scope
Predict phylogroups of Escherichia coli from genome assemblies.
This subworkflow uses ClermontTyping to determine the phylogenetic groups of Escherichia coli strains from assembled genomes. It processes each sample individually and aggregates the results into a single consolidated report.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Tab-delimited ClermonTyping phylogroup assignment results |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- clermontyping - Determine the phylogroup of Escherichia coli isolates.
Used By
This subworkflow is used by the following workflows:
- clermontyping - In silico phylotyping of Escherichia genus.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
ClermontTyping
Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microbial Genomics, 4(7), e000192. (2018)