MLST_pipeline: MLST pipeline for WGS assemblies July 3, 2024, Walter Demczuk...

In phac-nml/wade: Executes molecular typing on contig assemblies

MLST pipeline for WGS assemblies July 3, 2024, Walter Demczuk & Shelley Peterson

Description

Takes Organism, Sample Number, Locus, and a Variable at queries a contig.fasta file

Usage

MLST_pipeline(Org_id, Test_id, SampleNo, LocusID, curr_work_dir)

Arguments

Org_id	Organism to query: GAS, PNEUMO or GONO
SampleNo	Sample number associated with contig.fasta file
curr_work_dir	Start up directory from pipeline project to locate system file structure
locus	The locus to query, or enter list to use a list of alleles

Details

MLST pipeline: Takes Organism, Sample Number, Locus, and a Variable at queries a contig.fasta file vs downloaded pubMLST data.

Value

A table frame containing the results of the query

phac-nml/wade documentation built on Feb. 8, 2025, 3:02 a.m.