mcroni
Tags: mcr-1 colistin resistance promoter variant sample-scope
Scripts for finding and processing promoter variants upstream of mcr-1.
This subworkflow identifies and characterizes promoter variants upstream of the mcr-1 colistin resistance gene using mcroni. The tool searches for mutations in the promoter region that may affect expression levels of mcr-1, which is important for understanding the regulation of plasmid-mediated colistin resistance.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for mcr-1 promoter analysis |
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 mcr-1 gene variation results |
fa | Extracted mcr-1 gene sequence in FASTA format (optional) |
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.
- mcroni - Detect sequence variations in the mcr-1 colistin resistance gene.
Used By
This subworkflow is used by the following workflows:
- mcroni - Sequence variation analysis of mcr-1 genes (mobilized colistin resistance).
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) -
mcroni
Shaw L mcroni: Scripts for finding and processing promoter variants upstream of mcr-1 (GitHub)