MASTER_pipeline: Molecular typing pipeline for WGS assemblies December 21...
In phac-nml/wade: Executes molecular typing on contig assemblies

MASTER_pipeline

R Documentation

Molecular typing pipeline for WGS assemblies December 21 2023, Walter Demczuk & Shelley Peterson

Description

Takes Organism, Sample Number, Locus, to query a contig.fasta file

Usage

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

Arguments

`Org_id`	Organism to query: GAS, PNEUMO or GONO
`Test_id`	AMR, TOXINS, VIRULENCE, NGSTAR, use MASTER for 16S id
`SampleNo`	Sample number associated with contig.fasta file
`LocusID`	The locus to query, or enter "list" to use a list of alleles
`curr_work_dir`	Start up directory from pipeline project to locate system file structure

Details

GAS AMR loci:

dfrF, dfrG, DHFR, ermA, ermB, ermT, folA, folP, gyrA, mefAE, msrD, parC, rpsJ, tetM, tetO note that ermA == ermTR, ermC == ermT, mefA/E includes mefA and mefE; DHFR is the same as folA ermB + = ERY-R/CLI-R; ermT = ERY-R/CLI-?; mefA + = ERY-R/CLI-S; ermA/TR = ERY-R/CLI-Ind.

PNEUMO AMR loci: cat ermB, ermTR, folA, folP, gyrA, parC, mefA, mefE, msrD, tetM, tetO, pbp1a, pbp2b, pbp2x note that ermA == ermTR

GAS VIRULENCE FACTORS: covR => V128A covS => I332V; E226G (1228 deletion) rocA => V47A; R259Q; V333A; D396N; I404T; P405S rpoB/rgg => V169I nga => promoter mutations: A8G (K3R) or T13G (F5V) or C17T (A6V) (protein): F5V+A6V=pnga3 nga => D349G is the D330G mutation cpA, fctA, fctB, lepA and srtC1 all pilin proteins - use only fctA (major pilin protein) fbp54, grab, ideS_mac, mf_spd, speB, scpA, ska always positive? hasA,B,C are the same operon, use only hasA