genotyphi_parse

Tags: bacteria salmonella typhi genotyping mykrobe parser sample-scope

Parse Mykrobe results to genotype Salmonella Typhi.

Uses scripts from GenoTyphi to parse the JSON output from Mykrobe. It assigns isolates to specific S. Typhi genotypes (e.g., 4.3.1) based on the presence of specific SNPs defined in the GenoTyphi scheme.

Inputs

record (
    meta: Record,
    json: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
json	Path	The JSON output file generated by Mykrobe

Outputs

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 report containing the assigned GenoTyphi genotype
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

GenoTyphi Parameters

Parameter	Type	Default	Description
--genotyphi_kmer	integer	21	K-mer length
--genotyphi_min_depth	integer	1	Minimum depth
--genotyphi_model	string	kmer_count	Genotype model used. (choices: kmer_count, median_depth)
--genotyphi_report_all_calls	boolean	false	Report all calls
--genotyphi_mykrobe_opts	string	-	Extra Mykrobe options in quotes

Used By

Subworkflows

• genotyphi - Assign genotypes to Salmonella Typhi genomes.

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)

• McCortex
  Turner I, Garimella KV, Iqbal Z, McVean G Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 34, 2556-2565 (2018)

Source

View source on GitHub

Version

GENOTYPHI_PARSE:
    - mykrobe: 0.13.0