hicap

Tags: bacteria haemophilus-influenzae serotype capsule typing nthi sample-scope

Predict Haemophilus influenzae capsule serotype.

Uses hicap to identify the capsule locus in H. influenzae genome assemblies. It predicts the serotype (a, b, c, d, e, f, or Non-Typeable/NTHi) and can optionally generate visualizations of the locus structure.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

database_dir: Path?
model_fp: Path?

Name	Type	Description
database_dir	Path?	Path to a custom hicap reference database directory
model_fp	Path?	Path to a custom Prodigal training model file

Outputs

record (
    meta: Record,
    gbff: Path?,
    svg: Path?,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
gbff	Path?	GenBank file containing the annotated capsule locus region
svg	Path?	SVG visualization of the capsule locus gene arrangement
tsv	Path	Tab-delimited summary of the predicted serotype and locus coverage
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

hicap Parameters

Parameter	Type	Default	Description
--hicap_gene_coverage	number	0.8	Minimum percentage coverage to consider a single gene complete
--hicap_gene_identity	number	0.7	Minimum percentage identity to consider a single gene complete
--hicap_broken_gene_length	integer	60	Minimum length to consider a broken gene
--hicap_broken_gene_identity	number	0.8	Minimum percentage identity to consider a broken gene

Used By

Subworkflows

• hicap - In silico serotyping of the Haemophilus influenzae capsule locus.

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)

Source

View source on GitHub

Version

HICAP:
    - hicap: 1.0.4