Executes molecular typing on contig assemblies

Documentation for package ‘wade’ version 0.2.4

blast	Execute a given blast command
database_pipeline	Generic Profiler : SampleNo_contigs.fasta vs. arg-annot/resfinder2/CARD or VFDB
emm	emm typing pipeline from WGS assemblies
general_mlst_pipeline	Create a profile for MLST, NGMAST, or NGSTAR using blastn
labware_gono_amr	Run AMR first, then run the 23S allele counts, and then the NGSTAR-MLST analyses Then run this analysis to combine data from AMR, 23S rRNA and NG-STAR to prepare full amr profile to upload to LabWare.
master_blastr	Molecular typing pipeline for WGS assemblies
PneumoCaT_pipeline	PneumoCaT_Batch (Waffles version) : Log in to Waffles Download files from IRIDA using ngsArchiveLinker using folder structures Rename files to remove _001.fastq using: prename 's/_001.fastq/.fastq/' /.fastq Run command line to send all samples in the "fastqs" folder : $ for sample in 'ls fastqs' ; do sbatch -c 1 -p high -mem 4G -output $sample- $ watch sq CTRL-C to exit watch.
read_vcf	Reads a .vcf file ignoring any headers, creates a data frame from the remaining lines
rna_23s	rRNA.R