genotyphi
Tags: salmonella typhi genotype antimicrobial-resistance sample-scope
Assign genotypes to Salmonella Typhi genomes.
This subworkflow assigns genotypes to Salmonella Typhi genomes based on Mykrobe results using GenoTyphi. The workflow first runs Mykrobe for antimicrobial resistance prediction on sequencing reads, then processes the results with GenoTyphi to assign specific genotypes based on the presence of known genetic markers.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads |
lr | Long reads (ONT/PacBio) |
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 | A tab-delimited report containing the assigned GenoTyphi genotype |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- mykrobe_predict - Predict Antimicrobial Resistance (AMR) for supported bacterial species.
- genotyphi_parse - Parse Mykrobe results to genotype Salmonella Typhi.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- genotyphi - Salmonella Typhi genotyping with lineage assignment.
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) -
GenoTyphi
Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE, & International Typhoid Consortium. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid Nature Communications 7, 12827. (2016) -
Mykrobe
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook, DW, Iqbal Z Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe Wellcome Open Research 4, 191. (2019)