emmtyper

Tags: bacteria streptococcus-pyogenes gas typing emm virulence m-protein sample-scope

emm-typing of Streptococcus pyogenes (Group A Strep) assemblies.

Uses emmtyper to assign emm types to S. pyogenes genomes by blasting the assembly against a database of specific M protein gene (emm) subtypes.

Inputs

record (
    meta: Record,
    fna: Path
)

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

blastdb: Path?

Name	Type	Description
`blastdb`	`Path?`	Path to a custom emm cluster BLAST database

record (
    meta: Record,
    tsv: 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 summary of the assigned emm type and cluster
`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

Parameter	Type	Default	Description
`--emmtyper_wf`	string	`blast`	Workflow for emmtyper to use. (choices: `blast`, `pcr`)
`--emmtyper_blastdb`	string		Path to custom EMM BLAST DB.
`--emmtyper_cluster_distance`	integer	`500`	Distance between cluster of matches to consider as different clusters
`--emmtyper_percid`	integer	`95`	Minimal percent identity of sequence

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)
emmtyper
Tan A, Seemann T, Lacey D, Davies M, Mcintyre L, Frost H, Williamson D, Gonçalves da Silva A emmtyper - emm Automatic Isolate Labeller (GitHub)

EMMTYPER:
    - emmtyper: 0.2.0