rRNA23S_pipeline: 23S rRNA pipeline for WGS assemblies to determine number of...
In phac-nml/wade: Executes molecular typing on contig assemblies

rRNA23S_pipeline

R Documentation

23S rRNA pipeline for WGS assemblies to determine number of mutated alleles December 21 2023, Walter Demczuk & Shelley Peterson

Description

23S rRNA pipeline for WGS assemblies to determine number of mutated alleles December 21 2023, Walter Demczuk & Shelley Peterson

Usage

rRNA23S_pipeline(Org_id, SampleNo, curr_work_dir)

Arguments

`Org_id`	Organism to query: GAS, PNEUMO or GONO
`SampleNo`	Sample number or "list" or "folder" of sample numbers associated with VCF file(s)
`curr_work_dir`	Start up directory from pipeline project to locate system file structure

Details

23S rRNA pipeline for WGS assemblies to determine number of mutated alleles

E.coli: A2059G and C2611T

GONO: Run SNP core pipeline with NCCP11945_23S4.fasta file: A2045G or C2597T PNEUMO: Run SNP core pipeline with 23S_R6.fasta file: A2061G or C2613T

Takes Organism, Sample Number, Locus, and a Variable at queries a contig.fasta file #Parses 23s rRNA mutations from VCF files

ON GALAXY:

Alternative_allele_proporition = 0.1 min_coverage = 15 min_mean_mapping = 30 run_name = 23S in FreeBayes step of phylogeny set ploidy = 4

Export VCF from Galaxy: Under "Collection Tools" , use the tool "Export to Warehouse" on "Filter vcf on collection 210". It will bundle them together and makes a history item. They are in /Warehouse/Temporary/galaxy_exports/RANDOM_NAME. Click the "eye" to view RANDOM_NAME. You can then copy them from there using the regular file explorer into: " folder