EMM_pipeline: emm typing pipeline from WGS assemblies February 5 2024,...

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

emm typing pipeline from WGS assemblies February 5 2024, Walter Demczuk & Shelley Peterson

Description

emm typing pipeline from WGS assemblies February 5 2024, Walter Demczuk & Shelley Peterson

Usage

EMM_pipeline(Org_id, SampleNo, 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

Details

GAS emm typing: Takes Organism, Sample Number and queries a contig.fasta file. For the most current emm types go to: https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/ download the alltrimmed.fta file rename to "emm_trimmed.fasta" and place in the allele_lkup_dna folder in WADE GAS/emm then be sure to index it using MakeBlastDB

Value

A table frame containing the results of the query

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