ectyper

Tags: bacteria escherichia-coli serotype o-antigen h-antigen typing sample-scope

Predict Escherichia coli serotype (O and H antigens).

Uses ECTyper to identify the O-antigen (lipopolysaccharide) and H-antigen (flagella) genes in E. coli genome assemblies via BLAST. It provides a standardized serotype prediction (e.g., O157:H7).

Inputs

record (
    meta: Record,
    fna: Path
)

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

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited E. coli serotype predictions (O and H antigens)
txt	Path	BLAST allele details for serotype determination
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

ECTyper Parameters

Parameter	Type	Default	Description
--ectyper_opid	integer	90	Percent identity required for an O antigen allele match
--ectyper_opcov	integer	90	Minimum percent coverage required for an O antigen allele match
--ectyper_hpid	integer	95	Percent identity required for an H antigen allele match
--ectyper_hpcov	integer	50	Minimum percent coverage required for an H antigen allele match

Used By

Subworkflows

• ectyper - In silico prediction of Escherichia coli serotype.

Workflows

• ectyper - In silico prediction of Escherichia coli serotype.

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)

• ECTyper
  Laing C, Bessonov K, Sung S, La Rose C ECTyper - In silico prediction of Escherichia coli serotype (GitHub)

Source

View source on GitHub

Version

ECTYPER:
    - ectyper: 2.0.0