hicap
Tags: haemophilus influenzae serotype capsule cap-locus sample-scope
In silico serotyping of the Haemophilus influenzae capsule locus.
This subworkflow performs serotyping of Haemophilus influenzae by analyzing the capsule locus using hicap. The tool identifies capsule type and produces detailed annotations of the cap locus, including graphical representation in SVG format and annotation in GenBank format.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for H. influenzae serotype prediction |
database_dir: Path?
model_fp: Path?
| Name | Type | Description |
|---|---|---|
database_dir | Path? | Directory containing hicap reference database files (optional) |
model_fp | Path? | Path to HMM model file for improved detection (optional) |
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 |
|---|---|
gbff | GenBank file containing the annotated capsule locus region (optional) |
svg | SVG visualization of the capsule locus gene arrangement (optional) |
tsv | Tab-delimited summary of the predicted serotype and locus coverage |
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.
- hicap - Predict Haemophilus influenzae capsule serotype.
Used By
This subworkflow is used by the following workflows:
- hicap - Identify cap locus serotype and structure in Haemophilus influenzae assemblies.
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) -
hicap
Watts SC, Holt KE hicap: in silico serotyping of the Haemophilus influenzae capsule locus. Journal of Clinical Microbiology JCM.00190-19 (2019)